Minister for Agriculture Brendan Smith has said the Government will honour its commitments to farmers under the Farm Waste Management Scheme.
The Government had underestimated by €400m the amount it would have to pay to farmers under the scheme.
The scheme, which helps farmers carry out work upgrading slurry storage in line with EU rules, was introduced in 2006 with a deadline of 31 December 2008.
Mr Smith said his Department had budgeted for the grants according to the level of claims coming in, but there had been an unexpected rush of applications.
On RTÉ Morning Ireland, Mr Smith said he would have to talk to Minister for Finance Brian Lenihan, about the payments.
However, President of the Irish Farmers' Association Padraig Walshe said he could not understand how the Government underestimated what it would have to pay.
He said the number of applications would have been well known early last year and even earlier.
Mr Walshe said farmers have spent significant amounts of money upgrading facilities.
He said that in most cases, farmers have borrowed and the delay in making payments in 2009 is creating cashflow difficulties and pressures from lending institutions.
42,000 farmers have applied and around 34,000 have told the Department of Agriculture that they have completed work under the scheme, according to the IFA. Half of these farmers were already paid during 2007 and 2008.
