The Taoiseach was lobbied three years ago by the businessman with whom he was photographed in Kerry earlier this week.
Louis Moriarty, whose €20 million hotel development in Sneem Bertie Ahern visited on Tuesday, is at the centre of a series of investigations into illegal dumping.
Mr Ahern's constituency office also contacted the Environmental Protection Agency (EPA) over the activities of Mr Moriarty who is a constituent of Mr Ahern and who lives on Griffith Avenue close to Mr Ahern's home.
However, a spokesman for the Taoiseach said the contact with the EPA was initiated on behalf of residents living in the East Wall area of Dublin, who were having problems with a waste facility belonging to Mr Moriarty's company, Swacliffe Ltd, which traded as Dublin Waste.
The spokesman said that although letters relating to both contacts were signed by Mr Ahern, they were written by constituency staff and the Taoiseach was unaware of their contents.
Mr Moriarty has pleaded guilty and is awaiting sentencing relating to the biggest illegal dump uncovered to date in Ireland, at Whitestown in west Wicklow.
He and his company were also the subject of a High Court order to clean up another site, which contained hazardous and blood-contaminated hospital waste.
On Wednesday in a statement, the Taoiseach's office said Mr Ahern was unacquainted with Mr Moriarty before Tuesday's visit and unaware of his background.
Following queries from The Irish Times, a spokesman for Mr Ahern yesterday said that according to constituency records, Mr Moriarty visited a clinic in the Taoiseach's constituency. Mr Moriarty spoke to a member of Mr Ahern's staff and sought help in obtaining a waste permit.
At the time the businessman was the subject of High Court enforcement proceedings by the EPA to have his waste operations, based in Sheriff Street, shut down.
In January 2003, a letter was issued in Mr Ahern's name to Mr Moriarty informing him that: "I am precluded from taking any action in relation to this case as the matter is legal. I am sorry I can't assist you on this occasion."
Mr Ahern's spokesman said the Taoiseach's constituency office also phoned the EPA in 2002, following representations by East Wall residents about a waste transfer station operated by Mr Moriarty's company, Dublin Waste.
In June a letter was issued to the residents association in Mr Ahern's name outlining information given by the EPA about the enforcement actions taken against Dublin Waste.
Mr Ahern's spokesman said all of the contacts had been carried out by Mr Ahern's constituency staff and that the Taoiseach was "absolutely emphatic" he did not know Mr Moriarty.