Fianna Fáil TDs for Sligo-North Leitrim Dr Jimmy Devins and Eamon Scanlon have announced they are resigning the party whip.
The men said they are taking the action in protest at the Government's decision to transfer breast cancer services from Sligo General Hospital to University College Hospital Galway.
The two deputies had met the Taoiseach last week to discuss the situation.
Mr Devins said Brian Cowen did not believe keeping the services at Sligo General Hospital and having the unit 'networked' to University College Hospital Galway was an option.
Mr Scanlon said: 'After relentless lobbying by myself and the people of the northwest, I was unable to influence Minister [Mary]Harney of the justifiable case of the retention of the cancer services in Sligo General Hospital.'
Mr Cowen has said he regrets the decision by Mr Devins and Mr Scanlon, but that it was not possible to resolve the matters the men raised with him.
He added: 'The two deputies … continue to be members of the Fianna Fáil party and in that capacity I would hope and expect … they will be in a position to continue to support the Government.'
