Mr Flynn explained how he contacted the Revenue to dispose of the matter after deciding in 1998 not to contest any more elections.
He was minister for the environment when he received the cheque from Mr Gilmartin in May 1989 in the run-up to the general election. He later served as EU commissioner for social affairs from 1993 to 1999.
Both men dispute the circumstances in which the cheque was handed over.
Mr Flynn claims Mr Gilmartin intended it for his personal political campaign and that the cheque was already filled out and made payable to “cash”.
Mr Gilmartin claims Mr Flynn told him to leave the payee blank — but that he had intended the cheque go to Fianna Fáil.
Mr Flynn said he spent at least £40,000 on his 1989 general election campaign, contending he had spent £25,000 “and a good bit more” of the Gilmartin money on that election.
Patricia Dillon, counsel for the tribunal, noted Mr Flynn got his accountants to write to the Revenue in October 1998 with an accompanying cheque for £6,200 explaining the circumstances of the donation.
After the payment became public in 1998, Mr Flynn made a series of phone calls to the Luton-based developer. Cross-examined by lawyer for Tom Gilmartin, Jarlath Ryan, Mr Flynn denied the purpose of his calls was to get Mr Gilmartin to change his story that the £50,000 was a personal political donation.
He agreed with Judge Mary Faherty that the trigger for his calls were newspaper articles in September 1998 that an unnamed former FF minister had received £50,000 as a political donation. He was contacted by the tribunal in October 1998 but nobody in Fianna Fáil ever contacted him about the matter.
During one call he made to Mr Gilmartin on Sunday, September 27, 1998, Mr Flynn said he recorded Mr Gilmartin saying: “I told tribunal that Flynn had done nothing wrong.”
Asked why he was making the calls, Mr Flynn said he wanted Mr Gilmartin to confirm his memory of the events regarding the cheque was accurate.
Mr Flynn suggested that if Mr Gilmartin had told him he had got it wrong and that the cheque was for the Fianna Fáil party “they would have had the cheque by the next post.”
On October 1, 1998, Mr Flynn recorded Mr Gilmartin saying: “Told tribunal yesterday that contribution was for Flynn’s own campaigns because he liked him and was supportive.”
Ms Dillon stated that on October 2, 1998, Mr Gilmartin swore an affidavit that the money he gave to Mr Flynn was for FF.
Ms Dillon drew attention to a telephone conversation on September 29, 1998, where Mr Gilmartin was recorded saying there was “panic” and there was a meeting in Cork that day with Owen O’Callaghan.
Mr Flynn said he was not aware of such a meeting and Ms Dillon explained there was a Fianna Fáil convention in Cork on September 28.
The phone call note recorded Mr Gilmartin saying Mr Flynn “was to be ditched and that he had it from the horse’s mouth”. But Mr Gilmartin had not explained what he meant by this.
After Ms Dillon asked if the reference meant Mr Flynn was to be cut loose politically, he replied: “Nobody cuts me loose politically.”