The Moriarty report says Taoiseach Bertie Ahern and others may have wanted to "leave undisturbed" the facts behind a large payment made to Fianna Fáil on the day of the 1989 general election.
The previously unreported comment is made in a section of the lengthy report that deals with £75,000 given to then taoiseach Charles Haughey by businessman Mark Kavanagh that was intended for Fianna Fáil.
Only £25,000 was recorded by the party as having been received from Mr Kavanagh. The party's records showed the receipt for the donation had been given to Mr Haughey.
Tribunal chairman Mr Justice Moriarty describes as "extraordinary" the apparent fact that conversations seven years later in which Mr Ahern was involved did not lead to the discrepancy becoming known.
Last night a spokeswoman for Fianna Fáil said the party's legal advisers were studying the report. It was only when their work was complete that it would be known if the party could sue the Haughey estate for the return of money intended for Fianna Fáil, she said.
Mr Justice Moriarty's comments about Mr Ahern come in a section dealing with donations from Mr Kavanagh and Dr Michael Smurfit. Dr Smurfit said £60,000 he sent to a bank account in London in 1989 was intended for Fianna Fáil.
Around the same time Mr Kavanagh gave £100,000 to Mr Haughey. He told the tribunal he intended £25,000 to go to the Brian Lenihan fund and the rest to Fianna Fáil.
However, Mr Haughey gave only £25,000 to the party, which he said came from Mr Kavanagh. He gave the party another £50,000 which he said was from Dr Smurfit. He kept the remaining £25,000 from Mr Kavanagh and the £60,000 sent to London by Dr Smurfit.
In 1996 when the late Eoin Ryan snr was seeking to raise funds for Fianna Fáil from Mr Kavanagh, Mr Kavanagh complained he had never received a receipt for his 1989 donation. Mr Ryan told the tribunal Mr Kavanagh did not mention an amount.
Mr Ryan raised the issue with Mr Ahern and Mr Ahern spoke with the party's then financial controller, Seán Fleming. Mr Fleming told Mr Ahern the party had received £25,000 from Mr Kavanagh and that the receipt was given to Mr Haughey.
Mr Ahern subsequently met with Mr Kavanagh and apologised. He assured Mr Kavanagh that the donation had been received. Mr Kavanagh wrote out a new cheque to Fianna Fáil.
"What is extraordinary about these events is that it appears from the evidence of Mr Ryan, Mr Kavanagh and Mr Ahern, that in the course of all of the dealings between them, the discrepancy between the donation made and the donation recorded never arose," Mr Justice Moriarty said in his report.
He said it appeared Mr Kavanagh had never mentioned to Mr Ahern or Mr Ryan a donation of £75,000 and that Mr Ahern had never mentioned that the party records showed the receipt of only £25,000. The men had also not mentioned the role of Mr Haughey.
"The only reasonable explanations for all of these omissions are that: either those concerned were deeply embarrassed by what had occurred and chose to adopt a diplomatic approach to the issue or that there was a tacit understanding between them that the matter had arisen in a former era and that its details were best left undisturbed."
The Fianna Fáil spokeswoman said Mr Ahern did not want to comment on these observations.
Yesterday Mr Ahern responded to Mr Justice Moriarty's observation that Mr Ahern was "imprudent" when he signed blank cheques on the Fianna Fáil party leader's account during the Haughey era.
"If I ever for a moment had thought that by signing a cheque, which was a practice that everybody did in the country, let's be very frank and honest about it and not be prudish about it, I would have never signed them," he said.