The Taoiseach did not seek an apology from RTÉ over its TV news report on nude paintings of him, he confirmed in the Dáil today.
The portraits were displayed briefly on the walls of the National Gallery and the Royal Hibernian Academy gallery before they were removed.
One showed a naked Mr Cowen seated on a toilet and holding a toilet roll while the other displayed the Taoiseach holding his underpants in his hand.
Government press secretary Eoghan O Neachtain admitted complaining to RTÉ immediately after the news report on Monday evening of last week.
Gardaí later stepped in to quiz a 35-year-old teacher who claimed he painted the controversial artwork and an officer visited Today FM offices to seek email correspondence from the artist.
Speaking about the issue for the first time in the Dáil, Mr Cowen said: “In relation to the press secretary, he was not acting on my instructions or those of any minister and he did not seek an apology.
“RTÉ themselves decided to do that.”
Earlier, Fine Gael leader Enda Kenny sought clarification of the issue: “I’m asking a legitimate question about an officer who is appointed by the Government Information Service.
“All I want to know is did he ask: ’What you have done here to our Taoiseach is wrong. Please apologise.”’
“All he wants are the bare facts,” quipped Fine Gael TD Padraic McCormack.
Mr Cowen replied: “Well done Padraic. One of your better efforts.”
Labour deputy leader Joan Burton asked if it was appropriate for the Government press secretary to directly contact the director general of RTÉ.
Ceann Comhairle John O’Donoghue ruled the TD out of order as the issue was not relevant to Dáil business.
But Ms Burton asked how many times the Government press secretary has telephoned the head of the State broadcaster.
“Do you think that it is appropriate that the Government press secretary contact the director general in this way?
“I certainly sympathise with your family if they found the particular matter offensive.
“If the Government press secretary sees coverage on RTÉ of which he may disapprove, does he pick up the phone directly, as was done last week, to the director general of RTÉ?”
Ms Burton called for a clear distinction between the work of civil servants and political appointees.
Mr Cowen defended the 15 staff in the Government Information Service.
He said: “The media has moved from once having three national broadsheets and one national broadcaster to today’s media of 24-hour coverage and instantaneous access to information from newswires and websites.
“Today’s information from Government comprises paper press releases, emails, text messages, podcasts and webcasts.”