They claim there is an an €18m deficit in the semi-state peat company's super-annuation scheme.
Mr Cowen was in Tullamore attending the 13th International Peat Congress, a week-long event attended by 500 delegates from over 20 countries.
The pensioners from Offaly, Westmeath, Kildare, Laois and Longford protested outside the Tullamore Court Hotel.
Bord na Móna's managing Director says the company will make good the losses that have been incurred. But the protestors claim they have lost almost 25% of their pensions already and Bord na Móna has failed to invest in the scheme.
The Taoiseach said the pensioners' dispute is a matter for Bord na Móna to resolve, but on leaving the conference he stopped and spoke to pensioners protesting at the entrance to the hotel.
A spokesperson for the pensioners' group told RTÉ News that the Taoiseach had promised them that he would ask officials in his department to raise the issue with the company and try to expedite the matter.
The Managing Director of Bord na Móna, Gabriel D'Arcy, said the company is in the middle of reforming the two pension schemes it operates.
Mr D'Arcy said it will honour losses made in the general employee superannuation scheme, but wants to meet with the pensioners who protested this morning.
He said he was disappointed that the protest had taken place at an event that was not even organised by Bord na Móna, and that the pensioners had declined an invitation to meet with management of the company at lunchtime today.
The pensioners said they had declined the invitation because the company had taken 10 weeks to respond to the last piece of correspondence sent to it.
