The Taoiseach and Mr Ned O'Keeffe are in direct conflict over the discussions they had concerning his possible move to another Government department.
Mr Ahern told the Dail yesterday that he told Mr O'Keeffe he would move him to another Department if he was exonerated in relation to an alleged breach of ethics legislation.
However, while there was no public comment from Mr O'Keeffe last night, it is understood he maintains that the proposal to move him was not conditional on his exoneration.
Mr Ahern said Mr O'Keeffe, who resigned on Saturday, chose to go once it became clear that the inquiry would take considerably longer than expected. Mr O'Keeffe's version is that he resigned only when it became clear he was not going to be moved to another Department by the Taoiseach.
Mr Ahern agreed with Mr O'Keeffe's claim at the weekend that they had discussed moving him to another job but said this arrangement was conditional on Mr O'Keeffe's being exonerated. "On the basis that he was cleared I had no difficulty in him staying in his post, but as we know, things moved on," Mr Ahern told the Dail.
"I said to him that I believed that even if he was cleared by the commission that it would be better for him to move on from that Department."
However, he said "moving him on never arose" because the Public Offices Commission decided to launch an investigation into the matter.
He said Mr O'Keeffe had asked if he could talk to his family, prepare a statement and announce his resignation the following day.
"He and I agreed there would be no further talk about it. I made one comment on a request from the Government press secretary; I said I would be dealing with the issue.
"That was what I agreed with Deputy O'Keeffe. Unfortunately, the statements on Saturday morning upset Deputy O'Keeffe."
The national newspapers reported on Saturday morning that Mr O'Keeffe would be forced to resign or be dismissed.
This followed comments from Government sources that Mr O'Keeffe had been difficult to contact on Friday, that the Taoiseach did not believe he could do his job in the circumstances, and that Mr O'Keeffe did not seem to realise the seriousness of his position.