Yes.  Acts 15.15, 19, 24, 27-31.  Acts 16.4.  Matth. 18.17-20.

Well then, Do not the Brownists and Independents err, who maintain, that every particular Congregation, or church, hath in itself the full power of church Government for exercising the whole power of the keys, without subordination, or subjection to any Classical or Synodical Meeting: and that Presbyteries, and Synods, have only a power of counselling, advising, and exhorting, but no power of Jurisdiction, to command or enjoin any thing in the Lord, to particular churches or congregations?

Yes.

By what reasons are they confuted?

(1) Because, the Apostolick church referred all weightier matters, which did equally concern many Congregations, to the free suffrages and votes of the Apostles, Pastors, and select Brethren, and not to the determination of any one particular church, or congregation; Acts 15.23-25.  Acts 6.2,3. 

(2) Because, it is evident from Scripture, that there have been many particular churches, and congregations subordinate to one Presbytery.  For, in the church of Jerusalem, it is manifest, that there were more than one congregation. 

First, from the multitude of Believers, who were of a greater number than could be of one Congregation, for hearing the Word, and communicating; Acts 2.41,42.  Acts 5.14.  Acts 6.1-7.  Acts 21.20.  Secondly, From the multitude of Pastors and Ministers, whose pains and labours many churches required; Acts 1.12-14, 26.  Acts 2.1, 14, 37, 42.  Acts 4.31, 34, 35, 37.  Acts 6.2.  Acts 8.14.  Thirdly, From the diversity of Tongues among the Disciples at Jerusalem, which were given, not only for the edification of those that were of that Church, but also for signs and wonders to others, who were without, and not of that Church.  Fourthly, It is manifest from this, that in those days, they had no churches, or meeting houses built, but only met and convened in private houses, and upper rooms.

(3) The same is also true of the church of Antioch, Ephesus, and Corinth, from the Acts of the Apostles; and other places of Scripture.  But all these congregations were ruled and governed by one College of Pastors.

(1) Because, all these particular Congregations are called but one church; Acts 18.22.  Acts 12.5.  (2) Because, in that one church, there were church Presbyters, who were called Governors, not of any one particular congregation, but of the church, which was made up of many particular churches; Acts 20.17.  Acts 15.2,3.  Acts 13.1-3.  (3) Because, these Presbyters did meet together for governing the church, and performed Acts of Jurisdiction, which concerned the whole church in common; Acts 11.30, compared with chapter 4.35, 37: And Acts 21.18, 20-25, and Acts 13.1-3.  (4) Because, there is a particular example of a Synod, which had the power of Jurisdiction, and which consisted, and was made up of members, out of diverse Classical Conventions: For when the Question about circumcision, and the keeping of Moses’ Law, which troubled the Churches of Syria, Cilicia, Antioch, and Jerusalem, could not be determined in their own particular churches, the matter was referred to a Synod of Apostles and Presbyters, who met at Jerusalem, which decided the controversy, and appointed their decrees to be obligatory, and binding to all these foresaid churches; Acts 15.  Acts 16.4.  Acts 21.25. 

(4) Because, the Jewish church, which was a politick body, had in every city Synagogues subordinate to one supreme council, or great Synagogue which was at Jerusalem; Deut 17.8,12.  2 Chron. 19.8, 11.  Exod. 18.22, 26.  Seeing therefore, dangers and difficulties, for the preventing and healing of which, the Lord hath appointed and set up, in that church such a government, may be as great, if not greater in his church, under the New Testament than was then; and seeing the Lord has no less consulted the good of his church now, than he did of old; it follows, that there must be councils, no less under the New Testament than under the old, to which particular churches ought to be subordinate. 

(5) From the Light of Nature, and right Reason: for the Law of Nature directs to a diversity of courts; namely, where there is any Rule or Government in a city or common-wealth, and orders the inferior courts to be subordinate to the superior, the lesser to the greater, and Appeals to be made from them to the greater.  And in bodies both Natural and Politick the parts ought to be subject to the whole, for the good of both.  Beside there are, and will be very many Ecclesiastick affairs which will concern many Congregations equally and alike, which cannot be determined by any one.  (1st) Because, the Pastors and Presbyters of particular Congregations will stand in need each one of another’s help and assistance mutually.  (2ndly) Because, cases and difficulties may occur, more entangled, and intricate, than can be settled and composed by the Governors of any one Congregation.  (3rdly) Seeing particular Congregations which lie nigh one to another, ought to shun divisions, and differences, and to live in peace and unity, it follows manifestly, that there ought to be Synods or Councils, consisting of the Presbyters of many particular congregations, which ought to be subordinate, to these Councils, and Synods. 

(6) From Christ’s own precept, and command, Tell the Church; Matth. 18.15-17.  For if our blessed Lord appointed, that for a single brother’s offence, (he trespassing against GOD, or his brother, for gaining of him, and removing the Scandal) he be brought before the church, it follows by consequence, that the same course ought to be taken, when any one particular Congregation, offends against another, and remains obstinate in their scandalous Opinion, and Practice.  For our blessed Lord hath sufficiently prescribed a Remedy in this place, for removing of all Scandals and Offences, whether of one brother against another, or of one Congregation against another.  Nay, surely, since Christ hath consulted so much the conversion of one brother, that hath sinned, and gone astray; much more will he look to the good, and conversion of a whole Congregation. 

(7) Because, any one single congregation, with one Pastor only, hath not the power of Ordination, an instance whereof cannot be given, either from Precept, or Practice, in all the New Testament.  Nay, the Ordination of Ministers, in the New Testament, was always performed by a College of Pastors associate together; Acts 6.6.  Acts 13.1-3.  1 Tim. 4.14. 

(8) Because, from this doctrine of the Independents these and the like absurdities will follow:

First, that the Prophets must be censured, and judged by way of authority, not by other Prophets, but by the multitude and vulgar of the Congregation, which is contrary to 1 Cor. 14.32.

(2) That all the Councils, in the times of the Apostles, which were convocated upon necessary occasions for matters which concerned many churches alike, were but during the time, and extraordinary, and so not obliging succeeding churches, though the occasions, and causes, why these Councils were convocated then, are, and will be to the end of the world. 

(3) That private Believers, must be the Bishops of their own Bishops, Watchmen of their own Watchmen.  No communion or fellowship among Ecclesiastick Ministers.  That single and particular churches, though they have defiled, and puddled themselves, with the most black, and ugly Heresies, with the most abominable faults, and vices, yet are not liable to any Ecclesiastick Censure, but must be referred, to the immediate judgment of Christ, at the last Day. 

(4) That a College of Pastors, and Presbyters convened together from several congregations, shall have no more power of the keys of the kingdom of Heaven, than any one particular man, that is able to look to the good of his brother. 

(5) That a Pastor, out of his own Congregation, hath no power to administer the Sacraments, or to preach the Word, or exerce any Ministerial Act. — From which Absurdities, it follows evidently, that this kind of Church Government [asserted by the Brownists and Independents] labors under a manifest defect of the Means of Propagating the Gospel. 

(6) That Christ, hath as many visible bodies, as there are particular congregations.  That Men and Women, are to be accounted Members only of a particular congregation, and not of the Church-Catholick.  And that those who are excommunicated, are only casten out of a particular congregation not out of the Church Universal. [Which is all contrary to John 10.16.]

Quest. II. “MAY not the Ministers of the Church of themselves, by virtue of their office, meet in Assemblies, with other fit Persons upon delegation from their Churches, when Magistrates are open enemies to the Christian Religion?”

Yes.  Acts 15.2, 4, 22, 23, 25.

Well then, do not the Erastians err, who maintain, that the Ministers of the Gospel have no right or power in themselves, or by virtue of their office to meet in a Synod, or Council?

Yes.

By what reasons are they confuted?

(1) Because, the Church of GOD, in the primitive times, had power in themselves, to convocate their own Assemblies, for Worship and Government, not only without, but against the consent of the civil Magistrate, as is evident from the Acts of the Apostles, and Church Histories.  (2) Though the power, and right of meeting in church Assemblies be visible in the constitution, and exercise, yet it is intrinsic and within the church, as well as the power of Preaching.

Quest. III. “MAY Magistrates lawfully call a Synod of Ministers, and other fit persons to consult, and advise with, about matters of Religion?”

Yes.  Isa 49.23.  1 Tim. 2.1,2.  Matth. 2.4,5.  Prov. 11.14.

Well then, do not the Papists err, who maintain, that the civil Magistrate hath no right or power to convocate Synods, or Councils, but that it belongs to the Bishop to convocate Diocesan Synods; To the Metropolitan to convocate Provincial Synods; To the Primate and Patriarch to convocate National Synods: To the Pope only to convocate and call Oecumenick and general Synods?

Yes.

By what reasons are they confuted?

(1) Because, under the Old Testament, Councils, and Synods were appointed and called by godly Kings, 1 Kings 8.1.  2 Kings 23.1.  2 Chron. 29.4.  (2) Because, it is the duty of the civil Magistrate being born within the church, to take care that Peace and Unity be preserved and kept in the Church: that the Truth and Word of GOD, be entirely, and soundly Preached and obeyed: that blasphemies and heresies be kept under and suppressed; that all corruptions in Worship and Discipline be reformed: that all GOD’s Ordinances be lawfully established, administered, and preserved.  And if it should happen, that both Church and State Judicatories, should make an universal defection from the purity of doctrine and worship received and acknowledged, it is the duty of a godly King, by virtue of his Regal Power, and Authority, to set about a work of Reformation, and to call and command all ranks of People to return to the true Worship and Service of GOD; Isa. 45.23, [or 49.23.]  Psalm 122.7-9.  Ezra 7.23, 25-28.  Levit. 24.16.  Deut. 13.5, 6, 12.  1 Chron. 13.1-9, [or 2 Chron. 30.1-9.]  2 Kings 23, from the first verse to the 26th.  (3) From the example of Constantine, that did convocate the first Nicene Council:  From Theodosius the elder, that did call the first council of Constantinople: From Theodosius the younger, that did call the first council at Ephesus: From Martianus, that did call the Chalcedon council.

Quest. IV. “MAY all Synods or Councils since the Apostles’ days err?”

Yes.

And have not many actually erred?

Yes.

Well then, doth not the Popish Church err, who maintain, that councils confirmed, and solemnised by the Pope’s authority, cannot err, neither in explaining Doctrines of Faith, nor in delivering Precepts, and Rules of Manners, common to the whole Church?

Yes.

By what reasons are they confuted?

(1) Because, all the Priests, Levites, and Prophets of the Jewish church, (who had the same Promises which the Christian church hath now under the New Testament, 1 Cor. 10.3,4.  2 Sam. 7.16.  Isaiah 49.15,16,) together with the High Priest have sometimes erred, as is clear from the following Scriptures: Isaiah 56.10,11.  Jerem. 6.13.  Jerem. 14.14.  Hos. 9.7-9.  Micah 3.9.  The Lord’s Prophets that were immediately guided, and inspired by him, must be excepted.  (2) Because, councils under the Old Testament, lawfully called, have often-times erred; 2 Sam. 6.2-3.  Jer. 26.7-9.  1 Kings 22.6.  And under the New Testament; John 9.35.  John 11.47,48,52.  Matth. 26.57, 59, 65, 66. Acts 4.5, 6, 17, 18.  (3) Because, the Pope cannot shew a proof of infallibility; Rom. 3.4.  (4) Because, it is foretold in the New Testament, that many Pastors, and Teachers shall become false Prophets, and turn Seducers; and that Antichrist shall sit in the Temple of GOD, shewing himself that he is God; Matth. 24.11, 24.  Acts 20.29,30.  2 Peter 2.1.  2 Thes. 2.4.  (5) It is most evident, that many councils approven and authorized by the Pope, have most foully erred, and that some have openly contradicted others.