The Taoiseach has declined to comment directly on David Begg's comments today, ruling out a pay freeze among middle and low paid workers.
Speaking on his way into an IBEC dinner in Dublin tonight, Mr Cowen said Mr Begg was expressing his own view.
But Mr Cowen said that his job as Taoiseach, is to be sure that we are all aware of the emerging challenges, and that we use the benefits of social partnership to ensure we achieve an agreement that is mindful of the challenges we face.
Asked about the prospects of a wage agreement now, given today's comments, Mr Cowen said the stage of talking about pay has still not been reached.
He said discussions on non-pay issues were continuing and as the most up to date economic data becomes available, it will be used to inform future discussions on pay.
He added that there is no point in him conducting such negotiations in public.
When asked about government's vested interest in keeping the wage bill down, Mr Cowen said the Government had invested very heavily in public services in recent times.
As a result, he added, half the Government's total current bill comes from pay and pensions, and so it is obviously an important factor in the public finances.
The general secretary of the Irish Congress of Trade Unions had earlier rejected a call from the employers group, IBEC, for a pay freeze to help tackle economic recession.
In a robust response, Mr Begg said that IBEC had a brass neck to suggest pay restraint for low-paid workers at a time when many top executives were receiving millions in salaries.
He said Congress would make no sacrifices to continue the Social Partnership model.
David Begg was obviously angered by IBEC's call for a wage freeze.
He outlined increasing pressures facing the average worker - especially the low paid - including food and fuel increases, and hikes in interest rates.
He said for those people, a pay pause was a non-starter which he was not even prepared to entertain.
He stated that because of inflation, many workers had already endured a pay freeze - if not a pay cut - over the last 2 years.
He said he would not advocate sacrifices on behalf of workers to maintain social partnership in its current form - when others in society had their 'snouts in the trough'.
Congress was publishing proposals to address the economic crisis.
They include government action to tackle excessive prices, a 2% cut in the VAT rate, and food and fuel poverty programmes to assist those on social welfare.
