Legislation has been passed through the Dáil to allow for a banking inquiry by 123 votes to 11.
The Inquiries Privileges and Procedures Bill 2013 sets out a system for the Oireachtas to hold public investigations.
The Government successfully blocked proposals from opposition TDs, which the opposition claimed would have ensured the independence of proceedings.
The Fianna Fáil Spokesperson on Public Expenditure and Reform Sean Fleming, called for inquiries to always be chaired by a member of the opposition.
"You are insisting that the Government not only have a massive majority of the membership, but you also control the chair," Deputy Fleming said.
"And it won't be acceptable to say it will be a matter for the Oireachtas to decide, because the self-same Taoiseach controls the Oireachtas."
Yesterday, Minister Noonan warned banks that they must be prepared to hand over tapes of internal conversations to a parliamentary inquiry.
"The banks should be on alert, if they weren’t before, certainly from today, that this electronic data may be required by the Oireachtas inquiry committee," he said.