Officials involved in the EU-IMF bailout fear that Minister for Finance Michael Noonan's plan to impose losses on some Anglo Irish and Irish Nationwide senior bonds could have negative consequences on the ability of Bank of Ireland and AIB to raise funds in future.
Sources have told RTÉ News that the Irish Government did not consult the bailout partners prior to the Minister for Finance giving an interview to RTÉ in which he raised the possibility of burden-sharing with senior bondholders in the two failed banks.
Officials are concerned that if Ireland proceeded with the proposal, it could make it more difficult for AIB and Bank of Ireland to return to the bond market.
Stock market sources have also indicated that Mr Noonan's plan could dent Bank of Ireland's ambitions to sell shares to private investors in a rights issue.
The bank is privately hopeful of attracting some investment from private equity or a sovereign wealth fund as part of its attempts to raise €5.2bn of capital.
Most of the senior bondholders in Anglo and Nationwide are believed to be hedge funds, which bought bonds at discounts of their original value.
So, if the Irish Government were to repay the full value, those investors stand to profit.
It is understood there is some sympathy among the bailout partners for the Irish Government's concerns that future pay-out on unsecured and unguaranteed bonds in Anglo and Nationwide could result in significant profits for hedge funds at the expense of the Irish taxpayer.
A spokesman for the European Central Bank said: 'We are not commenting.'
He added the issue would be discussed with the Irish Government.
Earlier this week, Government sources said Minister Noonan would raise the issue of imposing losses with the EU and IMF in the autumn.
However, it is understood the bailout partners will now raise the issue with Irish politicians next month as part of a review of the aid programme.
One source said 'this issue will have to be cross-checked in July.'
It is understood the IMF has indicated it has little difficulty with losses being imposed on Anglo and Nationwide unsecured and unguaranteed bonds.
Mr Noonan's trip to the US was organised by the National Treasury Management Agency.
Asked if the NTMA has been made aware of Mr Noonan's plans to raise the issue of imposing losses on some senior bondholders, a spokesman for the NTMA said: 'We don't comment on discussions between the NTMA and the Minister.'
Yesterday Minister Noonan stressed there would be no burden-sharing for senior bondholders in AIB or Bank of Ireland.
Almunia to clear Anglo Irish's aid by June
Elsewhere, EU regulators will clear billions of euros in state aid granted to Anglo Irish Bank and Irish Nationwide Building Society by the end of the month, the European Competition Commissioner has said.
'I will be proposing a decision approving the aid for the resolution of Anglo and INBS by the end of this month,' Commissioner Joaquin Almunia said.
He said Bank of Ireland, AIB, Irish Life and Permanent, and EBS, which have completed capital and liquidity reviews, would have to present restructuring plans to the regulator by the end of July.
Mr Almunia also outlined his concerns on the market power of the Bank of Ireland and AIB.
'As a result of the Irish authorities' strategy to build the new banking system on two pillar banks, the Bank of Ireland and Allied Irish Banks will work in a de facto duopoly in the Irish market,' he said.
'As European Commissioner for Competition, let me say that this prospect will require close surveillance, because duopoly may hamper competition in Ireland's banking market,' he said.