The Tanaiste, Ms Harney, was not informed in advance that the Minister of State, Ms Liz O'Donnell, would refuse to support the Government in a vote in the Dail last week.
Party sources confirmed yesterday that Ms O'Donnell, Minister of State at the Department of Foreign Affairs, deliberately abstained in the vote on the private member's motion critical of Mr Ned O'Keeffe.
She was in Leinster House at the time but did not go into the Dail chamber for the vote on Wednesday night, according to a report in yesterday's Sunday Business Post.
It was the first time, they said, that Ms O'Donnell, as a Minister, took such deliberate action in a Dail vote.
The controversy over the operation of the O'Keeffe family farm erupted when it was revealed that pigs on the farm were fed meat-and-bone meal, under licences issued by the Department of Agriculture.
It was only following the vote that Ms Harney was made aware that Ms O'Donnell had not taken part. It is believed that at that point she made clear to Ms Harney that she had abstained because she was not happy with the situation, particularly as she did not know what action, if any, might be taken against Mr O'Keeffe.
The matter had been discussed at the PDs' parliamentary party meeting on Wednesday morning. Ms O'Donnell's Dail colleagues supported the Government in the vote. However, the matter was raised by the Tanaiste in a meeting with the Taoiseach, Mr Ahern, that day.
A spokesman for the party refused yesterday to reveal what was said by Ms Harney to Mr Ahern, declining to comment on the controversy.
The leader of Fine Gael, Mr John Bruton, described Ms O'Donnell's abstention as "a sort of a safe gesture".
"If she really intended it to be deliberate she would have said it before the vote rather than afterwards, when it is in nobody's interests to reopen the issue. I think there is an element of grandstanding on this."
The Fine Gael private member's motion called for immediate Government action on BSE. A Government amendment to the Fine Gael motion, approving the actions it is taking in dealing with the BSE problem, was carried by 72 votes to 62.
Government sources would not confirm yesterday reports that Mr O'Keeffe would be given a different portfolio or that a reshuffle of junior Ministers was planned.