Mr Lenihan stressed the report, which recommends €5.3 billion in public sector cutbacks, would remain “key to the budgetary process”.
It came after Ms Coughlan had told the Dáil many of the report’s recommendations “don’t make sense”.
Her views were echoed by Rural Affairs Minister Eamon Ó Cuív, who told Today FM, the opposition would love to see the Government implementing the report because some of its recommendations were “totally unacceptable”.
“Sorry opposition — not your day: we ain’t going to do them,” Mr Ó Cuív said.
But Mr Lenihan said Ms Coughlan’s intervention made little difference because the Government would still have to find €4bn of cuts in the budget.
He insisted that if individual departments did not agree with the report’s recommendations, they would have to provide alternatives.
He also appeared to suggest Ms Coughlan had merely been speaking in her capacity as Enterprise Minister rather than on the cabinet’s behalf.
Labour leader Eamon Gilmore said the conflicting views of Ms Coughlan and Mr Lenihan showed the Government was “in disarray”.
But Fine Gael leader Enda Kenny claimed Ms Coughlan had been speaking with the Taoiseach’s imprimatur and sending a clear signal that the Bord Snip report would be shelved.
Meanwhile, the chair of Bord Snip, economist Colm McCarthy, said he had no comment to make on the Tánaiste’s assessment of the group’s work.