By contrast, in presbyterian (and episcopalian) churches, the officers in each congregation are subject to the jurisdiction of higher church courts that hold them accountable. In presbyterian churches, congregational sessions are subject to presbyteries made up of the eldership of a number of congregations in the same region. Presbyteries, in turn, are subject to higher synodical assemblies composed of all the eldership in a larger area, an entire nation, the entire world, etc. The exercise of church leadership is seen as a collegial affair, with all the officers of the church subject to each other in mutually-binding councils. Presbyterianism (and episcopalianism) thus preserves a biblical accountability and mutual submission between congregations, officers, and members within the whole Body of Christ.
The website of Providence Presbyterian Church in Chilhowie, VA articulates these ideas on its website:
In accordance to the general principles of the Bible (see Acts 15) and because no church officer or church court is above error or abuse, Presbyterianism is committed to mutual accountability between officers and local congregations. Consequently, there are various levels of church government arranged in graded courts, each of which contains a plurality of both Teaching and Ruling Elders, who are obligated to rule and be ruled according to the Word of God and to submit to one another in Christian love.
However, as I've argued many times on this blog, the modern Reformed world is saturated with semi-congregationalism or denominationalism, which is the attitude that the legitmate, de jure church can exist in multiple independent denominations. Modern Reformed people, to a great extent, are comfortable with the idea that there are lots of denominations in the world with de jure legitimacy and authority--such as the OPC, the PCA, the FPCS, the FCC, the ARP, the FCS, the RPCS, the RPCNA, the URC, and so on--and that each of these have full legitimacy and authority in independence of each other, with none of them being subject to each other in mutually-binding councils. Thus, many modern Reformed people who oppose congregationalism actually practice independency themselves, but only at a higher level. Individual congregations are to be in mutual submission to each other, but only to a point. Groups of congregations (denominations) can be independent from other groups of congregations.
The problem with this is obvious. Semi-congregationalism does not preserve a full mutual accountability and submission of the brethren to each other. It does better than classic congregationalism, but it falls significantly short of the biblical requirement that all visible de jure churches be subject to all other visible de jure churches. Mutual accountability and submission doesn't get to stop at some arbitrary point, but it must exist within the entire de jure Body of Christ. So, in the end, many modern Reformed churches and officers are guilty of the same sort of thing they accuse congregationalist churches and officers of being guilty of. Only a full-fledged biblical presbyterianism can maintain full biblical accountability and mutual submission.
For more, see here and here. And see here for a couple of statements from churches that illustrate this semi-congregationalist attitude.