Legislation governing the country's universities is to be amended so that the Minister for Education can require them to comply with Government guidelines on remuneration and staffing numbers.
This follows recent reports of large sums being paid out in what the Department of Education regards as unapproved payments by colleges.
In a statement, Minister for Education Ruairi Quinn said no one sector should be able to operate outside of parameters laid down by Government.
Mr Quinn said he had secured Government agreement for changes to the Universities Act, which would strike a balance between university autonomy and protecting the economy at a time of crisis.
Between 2005 and 2009, around €7.5 million was paid in additional allowances by various universities to senior members of staff.
The new legislation will also give the minister powers to oblige universities to comply with collective agreements such as the Croke Park deal.
Trinity College Dublin has recently refused to implement a binding Labour Court finding under the provisions of that agreement.