Irish Ferries could collapse if an agreement is not reached between management and unions, the Irish deputy prime minister has warned.
The Isle of Inishmore has been in Pembroke Dock since Thursday
Mary Harney said the dispute, which has kept two ferries in Welsh ports for five days, put the future of the company at risk.
Crews on the ships are protesting at plans to replace staff with cheaper workers from abroad.
The company said it had to bring in foreign staff to remain competitive.
Taoiseach Bertie Ahern has also criticised Irish Ferries' handling of the row.
The Isle of Inishmore, moored in Pembroke Dock, and the Ulysses, docked in Holyhead, were due to sail last Thursday.
About 15 crew members are believed to be barricaded on each ship.
Speaking in Cork, Ms Harney called both sides in the dispute to stand back from the brinks and appealed to Irish Ferries to use industrial relations channels to bring about a resolution.
Informal talks between the management and unions took place on Monday at the offices of Ireland's Labour Relations Commission in Dublin.
After the talks, both sides stressed the negotiations were only the first stage.
An official for maritime union Numast, Tommy Molloy, welcomed the talks, but said he was cautious about the outcome.
"Obviously we're hopeful that that the talks will result in some kind of move towards settlement. Unfortunately it's very difficult to see what would convince them [Irish Ferries] to move," he said.
Some crew members seized control of the Isle of Inishmore after new eastern European crew boarded on Thursday.
Irish Ferries said the workers were there to familiarise themselves with the vessel and their roles.
The company said it had also placed security personnel on the ships to ensure the continued access of company staff and port officials.
Unions said the existing crew were upset by the manner of the security guards' appearance.
They claimed the men had boarded in Ireland as passengers, but had then changed into their uniforms in the toilets as the vessel approached Wales.
Irish Ferries said on Tuesday they had removed personnel security from the ships.
Crew member Gary Jones, who is on the Isle of Inishmore, told BBC Radio Wales on Monday that he and his fellow workers had "nothing left".
He said: "We've given a lot of things away to Irish Ferries over the last two years. They've made savings of £3.5m by taking away conditions from us.
"We've only our jobs left and that's what we're trying to secure."
Irish Ferries has said it had been completely open about what it was doing over bringing in new crews as part of a cost-cutting exercise. And it said it was justified in employing security staff.
Spokesman Alf McGrath said: "The security measures were necessary because in December of last year Siptu [Services, Industrial, Professional and Technical Union] staged two strikes... and totally locked up the ship in Holyhead and would not allow regulatory agencies or any management on to the ship.
"So we have a duty and responsibility to protect our assets."