The Taoiseach has said the Naval Service is short staffed and will be "cutting its cloth to suit the measure".
Leo Varadkar said he was briefed on the matter and that crews will now be spread across five ships instead of seven.
His comments follow a letter, published in the Irish Times over the weekend, in which Commodore Michael Malone said the ships' companies had spoken about the pressure they were under by not having the ships fully manned.
He said this was exacerbated by operating nine ships while only having the manpower for six-and-a-half ships.
Commodore Malone said he had taken the decision that the Naval Service now needed to "cut our cloth to measure".
He said he would achieve that by placing the LÉ Eithne and LÉ Orla in an operational reserve capacity until "adequate numbers of sufficiently qualified and experienced personnel are available".
In a response on twitter, Minister of State with Special Responsibility for Defence Paul Kehoe said the ships were in dock for planned maintenance and the crews were redeployed to other vessels.
Fianna Fáil's Defence spokesperson Jack Chambers said there has been "too much spin and deflection" on the retention crisis in the Defence Forces.
He accused Mr Kehoe of being in a "bunker of denial" over reports that two naval ships had been taken out of service due to insufficient crew numbers.
Minister Kehoe should immediately publish every naval ship maintenance schedule for 2019 to verify his new claims. There's been too much spin and deflection on this ongoing retention crisis https://t.co/V46nlRnReO— Jack Chambers TD (@jackfchambers) July 7, 2019
Meanwhile, a spokesperson for the Taoiseach said this evening that: "The Irish Naval Service has 9 vessels; 1 of which is in refit and 2 are going into maintenance. Crew will be redeployed from these vessels so six vessels will be fully crewed.
"It is never the case that all 9 vessels would be at sea at the same time.
"As both the Taoiseach and Minister Kehoe have pointed out, the staff shortages in the Naval Service are well recognised; that is one of the reasons the Government announced a €10m package for our Defence Forces last week. This is in addition to full pay restoration for rank and file members of the navy in line with other public servants in 2020."
Speaking on RTÉ's Morning Ireland, Mr Chambers said he was quite surprised that Minister Kehoe would so publically dismiss the concerns of such a senior officer in the Defence Forces.
Naval Service : I have spoken to the Chief of Staff of the Defence Forces this evening about ongoing challenges in the Naval Service.— Paul Kehoe T.D (@campaign4kehoe) July 6, 2019
Vice Admiral Mellett reconfirmed that two of our vessels are in dock for planned maintenance.The crews have been redeployed to other vessels.1/2
Nevertheless, we both recognise the personnel difficulties facing the Naval Service and we have agreed that these matters will be prioritised at a meeting involving civil and military leaders next week. 2/2.— Paul Kehoe T.D (@campaign4kehoe) July 6, 2019
"For the minister to undermine a senior staff member is a very serious development.
"Paul Kehoe said that no ships were tied up due to manpower issues - I think he needs to stop playing a game of pretend with our Defence Forces.
"If we only have manpower for six- and-a-half ships, but we have nine ships, how on earth does anyone believe him when he says there's no manpower issues?"
Mr Chambers said Minister Kehoe has "inappropriately involved" Chief of Staff Vice Admiral Mark Mellett, into the equation by referencing him on Twitter.
He called on the minister to show honesty, integrity, and transparency.
He said the naval service has been "hollowed out" and cannot now perform its basic duties.
In a statement, the department said: "Issues pertaining to the Naval Service will be discussed at a meeting of civil and military leaders this week.
"The focus of the minister is on charting the return of the Naval Service to full capacity. This will take time. He will be kept briefed on the considerations of the Civil/Military group.
"Rest assured , this is of huge priority."
The CEO of Irish Water Safety and formerly, a Lieutenant Commander in the Irish Navy, John Leech, has said he is concerned about further deterioration of staff levels in the Naval service.
Speaking on RTÉ's Six One News, Mr Leech said that the Aer Corp had introduced a range of improvements to pay and conditions some years ago and a similar initiative is needed for the Naval service conditions were improved for the Aer Corp and something similar will be needed to improve staff levels in the Navy.
He said that the package announced by the government for the Defence forces will not be enough to attract new members.
Mr Leech said that improvements in conditions also need to be made.
He said that fewer staff resulted in shorter time off when vessels returned from patrol assignments.
Mr Leech said that Royal navy personnel have much more time off after returning from patrol duties.