The Taoiseach, Mr Ahern, has said he "deeply regrets" the decision of Ryanair not to co-operate with the Labour Court in its efforts to find a settlement to the dispute between the airline and its baggage-handlers.
He said the failure to resolve the dispute was calling into question the social partnership system.
Mr Ahern said the prolonged dispute was a matter of grave disquiet and he hoped it would soon be resolved in a spirit of co-operation and social partnership.
"I do not believe a tooth-and-claw-style capitalism is the direction in which most people want the Celtic Tiger to go. We need a real impetus on both sides to engage in real dialogue, with thirdparty help, offered by the State if that is required," he said.
Mr Ahern's comments are the strongest statement yet from the Government on the five-week dispute at Ryanair over pay and conditions and union recognition. He warned that failure to resolve the dispute "has even called into question the efficacy of social partnership arrangements".
A Ryanair spokeswoman repeated the company's position, saying it had not accepted the Labour Court's invitation to intervene in the dispute as quite a number of its people had begun to return to work and it did not wish to disrupt this process.
Addressing the Cork Chamber of Commerce annual dinner, Mr Ahern said he appreciated the huge contribution Ryanair had made to the economy in the 12 years since its foundation, especially to the surge in tourist numbers.
But, he said, the trade union movement had also made a major, positive contribution to underpinning strong growth.
Mr Ahern said he had always been an advocate of responsible trade unionism and responsible trade union participation in social and economic affairs.
"While I respect the decisions of some global firms that can offer first-class conditions to operate alternatives acceptable to their workforce, in other cases, other things being equal, it is preferable that larger companies can accommodate the presence of trade unions," Mr Ahern said.
Sources say accommodating unions and recognising them is not quite the same thing, and the issue is a sensitive one for many multinationals with operations in Ireland.
IDA Ireland companies are invited to meet trade unions when they come here, but union recognition is not something that the IDA can force on them. While many prefer to deal directly with their own employees rather than use third-party intervention, some are prepared to accommodate unionised employees, while often not recognising the union as the party with which to negotiate contracts and pay issues.
Mr Ahern also touched on the issue of management bonuses in his address. He said nothing was more calculated to create problems than top management denying its workforce a structured system of negotiation while receiving colossal financial rewards.
"All firms must be aware of the value of a positive industrial relations image, whether they are unionised or not," Mr Ahern said.
There has already been controversy over the bonuses paid to the Ryanair chief executive, Mr Michael O'Leary.
At the time of the company's flotation last May, it was revealed that he had made £17 million over the previous three years through a company bonus scheme.