Suggested resource: "Don't Fire Your Church Members: The Case for Congregationalism" by Jonathan Leeman
Among Protestant churches there are basically three types of church government: the episcopal, the presbyterian, and the congregational.
In the episcopal system the chief ministers of the church are bishops while local congregations are served by presbyters (or priests) and deacons. Each of these offices are mentioned in the New Testament although those who adhere to either the presbyterian system or the congregational argue that the Scriptural offices of bishop and presbyter are actually different words for the same office. Those in the episcopal system (which includes Episcopalians, Anglicans, Methodists, and Catholics as well) argue that the pattern in the NT is that the apostles were operating in the role of bishop as they appointed elders in each church.
Those in the presbyterian system focus on the work of elders (bishops/presbyters) in the local church. Each church elects a "session" of elders who oversee the affairs of the church. The head pastor is elected by the congregation but is ordained by the presbytery which consists of the teaching and ruling elders from a group of congregations over which it exercises jurisdiction. They argue that this model is provided in the Scriptures where in each city there appears to have been a group of presbyters who formed a kind of college or committee which was in charge of local church affairs. They believe this makes the best sense of exhortations of Heb. 13:17 and 1 Thess. 5:12 - 13 and follows the model of the Council of Jerusalem in Acts 15.
Congregationalists, on the other hand, argue that we see in the New Testament autonomous congregations which were not subject to episcopal or presbyterial control. The apostolic authority we see in the New Testament is reflective of the fact that they were apostles set apart by Christ and they were the founders of the first churches. After their death, there were no apostles to take their place. Instead, congregations were self governing under the leadership of each congregation's congregationally chosen elders (prebyters/bishops). Congregationalists point to ancient documents such as The Didache to argue that this was the model of the earliest churches.
Baptist churches are congregational churches.
While in a congregational system the congregation makes the final decision in certain matters, we cannot forget that Jesus is the head of the church and we have been given the Scriptures as our infallible guide for belief and practice. Not only that, but Jesus has appointed a group of men, the elders, to teach and lead the church in His stead.
That beings said, in a congregational system, the congregation is considered the final court of appeal in matters of discipline, doctrine, personal disputes, and church membership. It is in these areas that church members cast votes and make corporate decisions.
There are at least six arguments for a congregation system of church government:
1) Matthew 18:15-17
If your brother sins against you, go and tell him his fault, between you and him alone. If he listens to you, you have gained a brother. But if he does not listen, take one or two others with you, that every charge may be established by the evidence of two or three witnesses. If he refuses to listen to them, tell it to the church. And if he refuses to listen even to the church, let him be to you as a Gentile and a tax collector.
The final court of appeal in a matter of discipline is not the pastor or board of elders nor is it an entity outside of the church, but the entire gathered congregation.
2) Matthew 16:13-19 and 18:18
Now when Jesus came into the district of Caesarea Philippi, he asked his disciples, "Who do people say that the Son of Man is?" And they said, "Some say John the Baptist, others say Elijah, and others Jeremiah or one of the prophets." He said to them, "But who do you say that I am?" Simon Peter replied, "You are the Christ, the Son of the living God." And Jesus answered him, "Blessed are you, Simon Bar-Jonah! For flesh and blood has not revealed this to you, but my Father who is in heaven. And I tell you, you are Peter, and on this rock I will build my church, and the gates of hell shall not prevail against it. I will give you the keys of the kingdom of heaven, and whatever you bind on earth shall be bound in heaven, and whatever you loose on earth shall be loosed in heaven."
"Truly, I say to you, whatever you bind on earth shall be bound in heaven, and whatever you loose on earth shall be loosed in heaven."
Congregationalists understand the "rock" of 16:18 to be the confession that Jesus is "Christ, the Son of the living God" as confessed by Peter who is representative of the disciples and those who would come after them, the church. The is evidenced by the language of "binding" and "loosing" being used in relation to both Peter (16:19) and the church (18:18).
Given the context of Matthew 18:15-18 and comparing it to the conversation of Matthew 16:13-19, we understand that the church's possession of "the keys" means that the congregation has the ability and duty to affirm or reject confessions of faith and, in doing so, render judgment on the confessor. Based upon this judgment, the congregation can open the door to an individual's continued fellowship with the body of believers or they can shut and lock the door forbidding that individual's fellowship with them. We see this in action in Acts 15 (understanding the Jerusalem Council to be a temporary situation when the apostles were in a unique position of planting the first congregations) as well as reflected in Paul's admonition of 1 Corinthians 5. There is no mention of these actions being taken by bishops or pastors but, instead, the keys were given to the gathered church.
3) 1 Corinthians 5
A situation involving sexual immorality exists within the church in Corinth and Paul, who has already personally passed judgment on the situation (vs. 3), does not take action himself but, instead, calls the congregation to judge the situation and expel the guilty party from their midst. This is the first two points put into action. The church apparently did so by majority vote as reflected in Paul's statement of 2 Corinthians 2:6: "this punishment by the majority is enough."
4) 2 Corinthians 2:5-11
Now if anyone has caused pain, he has caused it not to me, but in some measure- not to put it too severely- to all of you. For such a one, this punishment by the majority is enough, so you should rather turn to forgive and comfort him, or he may be overwhelmed by excessive sorrow. So I beg you to reaffirm your love for him. For this is why I wrote, that I might test you and know whether you are obedient in everything. Anyone whom you forgive, I also forgive. Indeed, what I have forgiven, if I have forgiven anything, has been for your sake in the presence of Christ, so that we would not be outwitted by Satan; for we are not ignorant of his designs.
Seeming to address the situation of 1 Corinthians 5, Paul urges the congregation to accept back the individual who had committed the sexual sin. The congregation had expelled the individual (2:6) and this discipline had its intended effect of bringing them to sorrow and repentance (2:7). Again, the "keys" are put into practice. He had been locked out from their fellowship but now the door was being opened once again.
5) Galatians 1:8
Even if we or an angel from heaven should preach to you a gospel contrary to the one we preached to you, let him be accursed.
The congregation is charged with guarding the doctrine of the church. If doctrine that runs counter to the gospel is preached, they are to reject the teaching and the teacher- even if it is the apostle Paul or an angel! This points to the need of congregations to be given the ability, through their church constitution and bylaws, to remove errant pastors.
6) Acts 14:23
And when they had appointed elders for them in every church, with prayer and fasting they committed them to the Lord in whom they had believed.
The gathering of believers was considered a church even though they did not yet have elders. Until an elder was appointed (and after!), the congregation would have had the authority and duty to follow points 1-5 above.
These six passages not only give evidence to support a congregational system but highlight what in particular the congregation is responsible for. Contrary to what many assume, in a congregational system, the members of the church don't vote on everything a church does. This is because the ultimate responsibility for everything a church does falls not on them, but on the elders they elect (see Hebrews 13:17 and Ephesians 4:12) and the elders must have the ability to lead as they believe God is directing them as long as they do not preach a false doctrine or disqualify themselves from ministry by their words or actions. In cases such as that, the congregation serves as a type of emergency brake for a church which is careening out of control.
But the congregation should embrace the responsibilities it does have toward one another. Typically, in a congregational system, candidates for membership in the church are voted on by the congregation. This is not a mere formality, but the means by which a congregation communicates to the new member that they are embracing the responsibility of stewardship for them that members have for one another. Members are called to encourage, disciple and, at times, discipline fellow members. The congregation, by voting “yes,” are communicating that they take that call seriously and that the new member has a right to expect such treatment. Again, this is no formality, thus the “yes” cannot be assumed to be automatic. The candidate should be examined in order that the congregation can be confident that they do, indeed, confess Christ as Savior and that their lives give validation to their confession. If the time does come when the congregation must discipline a fellow member, their duties towards them do not end. Rather, they have a duty to treat them as a “Gentile and a tax-collector (i.e. an unbeliever) and to call them to repentance in the hopes that they will be restored in their faith and, as a consequence, restored to a healthy relationship within the church.
Caleb Greggsen and Sam Emadi helpfully note that:
More fundamentally than any vote, congregationalism is about the member who of his own initiative starts reading the Bible with a new convert. It’s about the member who out of her own heartbreak over sin’s effect on the church urges a fellow member towards repentance. It’s about the member who utilizes the body to pray for her unbelieving coworkers. Any church leader in any kind of polity values these sorts of things. But only congregationalism recognizes that these kinds of activities are the essence of what makes a group of Christians a church.