The Labour leader also said this could apply to the Central Remedial Clinic after recent revelations that it had €14m in its account and had used funds raised to top up officials pay.
Amid reports that a €113m savings review of medical cards is to be revised downwards, Mr Gilmore said it had yet to be decided how exactly health savings would be made next year.
Speaking at the end of his party’s three-day conference in Killarney, Co Kerry, he said the first priority ahead would be the creation of employment.
Delivering his televised speech on Saturday night, he said Labour was all about fixing things and suggested that workers could be in line for some tax breaks.
Around 1,000 Labour delegates attended the conference, debating motions on the economy, health, taxes, and the environment among other issues.
“The crisis is not all fully fixed yet, but because of the progress we have made, we can now at last begin to look forward to post-recession Ireland,” he said.
Mr Gilmore emphasised it was Labour’s ambition for the country to return to full employment. He also stressed the work that the coalition had done and the exit from the troika bailout later this month.
“This was a moment of national crisis which required of us to think not about the next election but about the next generation.”
Speaking at the end of the conference, he laid out a warning for agencies breaching pay guidelines. Following revelations at an Oireachtas committee on pay to officials in state-funded hospitals and clinics, he said transparency was needed and that agencies funded by taxpayers should comply with public pay policies.
He added: “Yes, one of the options open to government if there is not compliance is to make reductions in the level of funding that is provided to them.”
Asked if there were any contractual issues which stopped the Government interfering, Mr Gilmore said public service salaries had already been cut.
“That has been in government, across the civil service, across all of the state agencies. It is our strong view that agencies that are also funded by the taxpayer, that have a role in the delivery of services, they should also comply with public pay policy.”
He said he was surprised about the revelation of top-up payments and the accounts of the Central Remedial Clinic. “That is one of the agencies that is going to have to be looked at.”
Despite his Education Minister Ruairi Quinn calling for the board of the CRC to resign, Mr Gilmore did not go as far as this and instead said they needed to provide answers about their funds. “That’s the first thing that we need to see from them.”
Mr Gilmore also dismissed reports that €113m savings planned through a review of medical cards would be reduced.
Despite weekend reports that the medical card probity target could be lowered by a third, he added: “That’s an issue that will be addressed in the context of the service plan. It is with the Minister for Health and he will bring it [the plan] to government.”