Complex sentence: The collegiums (i.e., ministries) and the Senate, instituted by Peter the Great as supreme governing bodies, were not called "governing" any more and were held accountable before the Council rather than the Emperor.
Split into simpler sentences: The collegiums (i.e., ministries) and the Senate, instituted by Peter the Great as supreme governing bodies, were not called "governing" any more. They were held accountable before the Council rather than the Emperor.