A spokesman for the European Commission said the pricing elements for Ireland's rescue package were agreed by member states, including Ireland, in May.
Amadeu Altafaj, Spokesman for EU Economic and Monetary Affairs Commissioner Olli Rehn, said the elements were a condition for the loan mechanism to be set up.
He was responding to RTÉ's report on the 3% margin being applied to part of Ireland's rescue deal.
Mr Altafaj said it was agreed by member states that the interest rate for the EFSM component of any rescue package would be equivalent to that applied by the IMF.
When asked if the margin was at odds with the spirit of solidarity enshrined in Article 122 of the EU treaties - upon which the EFSM regulation is based - Mr Altafaj said that the interest rate of 5.7%, incorporating the 2.925% margin, was still cheaper than the market rate.
The EFSM is the European Financial Stabilisation Mechanism, which forms one part of the overall €750bn rescue plan agreed by euro zone finance ministers in May.
Under the mechanism, the European Commission raises money on the international market on behalf of a member state using its AAA credit rating.
Mr Altafaj said that the interest rate charged to the Commission to raise the money would be 'under 3%'.
When added to the margin of 2.925% this brought the total interest rate for the EFSM segment of the rescue up to 5.7%.
The margin was included in the overall interest rate in order to ensure a swift return by the member state to the market.
'It is a way to incentivise a return to the market, and to disincentivise a country which might be tempted not to take the effective action to avoid a deterioration in its public accounts,' Mr Altafaj said.
RTÉ News has been told by Ireland's representative on the European Court of Auditors that this is the first time the EU has ever imposed a profit margin on money it has loaned or has guaranteed.
Gilmore questions 'penalty rate'
Labour leader Eamon Gilmore asked in the Dáil why Ireland was being asked to pay such a high rate of interest and why Finance Minister Brian Lenihan had agreed to it.
Responding to criticism about the 3% level of interest, Mr Cowen said that what was available under the deal is comparable to what is available from the cheapest source of international credit, the IMF.
He said to talk about the rate being a penalty was a misnomer and that it was important to recognise that the 'lender of last resort facility' was available to Ireland for the first time since the 27 member states set up the mechanism.
He said that the other countries were being loaned money under the stabilisation facility that applied to euro zone countries.
Mr Gilmore told the Taoiseach that EU was not just helping Ireland but the deal was also designed to support the Euro. He therefore asked why Ireland agreed to paying the penalty rate of interest.
The Taoiseach said this was the first time this situation had arisen in Europe and that there was no alternative to the deal being offered by the EU.
Sinn Féin Finance Spokesperson Pearse Doherty last night accused the EU of profiteering on the back of Ireland's economic difficulties.
Mr Doherty called on all TDs to 'reject this deal out of hand' when it comes before the Dáil today.
In a statement, Mr Doherty said: 'Far from coming to Ireland's rescue the EU is profiteering on Ireland's economic difficulties.
'We are now being told that there will be an additional 3% profit margin, or €5bn for the EU for the courtesy of Ireland bailing out European banks.
'This is a completely unacceptable situation.'
