As part of his attempt to combat "aggressive secularism" in Irish society, he issued invitations to Catholic bishops, the Church of Ireland, the Jewish Chief Rabbi and Muslim leaders to take part in multi-faith talks.
But the Church of Scientology, which counts film stars such as Tom Cruise and John Travolta among its members, was left out.
According to documents obtained under the Freedom of Information Act, its Irish representative Gerard Ryan, wrote a letter of protest to Mr Ahern asking whether this had been a "pointed snub".
"Perhaps this was simply an error of omission, and if so, I apologise for any inference I may have inadvertently made.
"However, if our church was deliberately not invited I would greatly appreciate if you would tell me why," he wrote.
A spokesman for Mr Ahern wrote back in March last year to say that the letter would be brought to his attention -- but there was no further communication with the church.
The scientologists had previously sent a DVD entitled 'This is Scientology' to Mr Ahern's department and offered to meet officials at any convenient time to discuss "issues of mutual concern".
Utopia
It says "the aims of our Church include the creation of a civilisation without war, crime or insanity, and whilst such an apparent utopia may seem unduly optimistic, nevertheless we have achieved some expertise in the handling of such issues."
The Church of Scientology claims to have millions of members across the world, but critics have accused the organisation of financially exploiting its members by charging them fees to access information and resources.
Mr Ahern set up the church-state dialogue process after a highly publicised speech in 2005, in which he condemned "aggressive secularism" for marginalising the role of religion in society. He invited the leaders of 15 Christian churches as well as Jews, Muslims, Baha'is and humanists to Dublin Castle for the launch last year.
Mosque
The FOI request for letters sent to Mr Ahern's department also revealed that the Cork Muslim Society attempted to enlist his help in getting a permanent mosque in the city. Its vice president Dr FW Radwan, pointed out that it had to use a rented premises for its 5,000 members.
Mr Ahern received a letter from Archbishop Brady of Armagh last June congratulating him on his re-election as Taoiseach.
He also received a personal letter from Bishop Edward Daly, perhaps best known for his role in helping the wounded on the day of Bloody Sunday in Derry in 1972.
He thanked Mr Ahern for his visit to the cross-community Foyle Hospice in Derry last year and his "major and significant role" in the peace process.
According to the correspondence, Archbishop of Dublin Diarmuid Martin wrote to Mr Ahern to invite him to attend Mass to mark World Peace Day on New Year's Day.
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