A "very small number of people" who come and go from the State are being monitored for Islamic terrorism-related activity, Bertie Ahern told the Dáil.
Reports that there were six units active in Ireland were misleading.
"You would think it was six active cells" but in reality "there are a very small number of people who are very closely watched and monitored and considered to be high-classified people who do come and go from this country".
He said these individuals were engaged in logistical and financial support.
Mr Ahern was replying to Opposition leaders on a report released to RTÉ through US Freedom of Information legislation that in 2003 there were six Islamic terrorist-related units operating in Ireland.
Fine Gael leader Enda Kenny asked if the Taoiseach was "given any briefings on this by the American government. Obviously, if the CIA or the FBI or the Homeland Security people in the States are aware of Islamic terrorists groups operating throughout the world, they would have evidence in respect of Ireland".
He also asked the Taoiseach: "Can you give the House an assurance as far as possible that there are no clandestine cells operating in Dublin and in Ireland, delivering logistical support and financial arrangements to international terrorist groups?"
Labour leader Pat Rabbitte said "there is a certain irony that the information was secured through the American Freedom of Information legislation and not something that could happen in this jurisdiction". He asked if "these groups are still operating here" and what was the "current assessment of the risk, if any, posed as a consequence?"
Mr Ahern said since 2001 there were operational activities by gardaí "on a small number of suspects linked to al-Qaeda".
Gardaí had reported back to the Government from time to time that they had been monitoring "very small groups, mainly individuals".