The closure of the Teagasc centre at Ballinamore, Co Leitrim is an operational matter for the board of the research and development organisation, the Taoiseach has told the Dáil.
As farmers blocked the gates of the building in an ongoing protest against its closure and the removal of the facility's herd of cattle, Mr Ahern said it would "not be appropriate for me to direct or ask the Minister to interfere with what is a functional decision of the board of Teagasc".
Mr Ahern said he understood the facility was a field station rather than a research centre and that three people were involved full-time there.
He was responding to Mr Joe Higgins (Soc, Dublin West) who called for the Taoiseach to urgently intervene in the situation where the local community was being "bullied".
Mr Higgins said that a "huge deployment of gardaí has also been present for the past few days to bludgeon the community into line with the disastrous decision of the Minister for Agriculture to cut the Teagasc budget in 2002".
This would end "vital research" which touched on the "livelihoods of the small farming community and workers in the more marginalised and disadvantaged areas which involve a band of counties", and it followed just two years after €250,000 was invested in the facility.
The Taoiseach said however the decision was not due to lack of funds because Teagasc had recently sold its centre in Sandymount, Dublin for €20 million and was moving to Carlow because "there are no farmers left in Sandymount".
He added that farmers involved in the Teagasc board believed it was the best thing to do, but Mr Billy Timmins, Fine Gael's agriculture spokesman, said that farmers' representatives had been against the decision.