Mr Shatter had made a public statement after the 'Prime Time Investigates' show last May falsely accused the Galway priest of rape and of fathering a daughter with a Kenyan woman.
Mr Shatter said in the statement that he had watched the programme with a "sense of revulsion" at the unspeakable catalogue of abuse against children it had revealed.
"I share the widespread public concern and disgust at the revelations which the programme contained," he said.
Mr Shatter also contacted Garda Commissioner Martin Callinan about the programme -- saying that people were entitled to be reassured that everything was being done to counteract this "evil" where ever it took place.
But yesterday, Fr Reynolds's solicitor, Robert Dore, said it had been "rash and premature" for Mr Shatter to issue such a statement.
"It would be desirable for Mr Shatter to clarify that he accepts that Fr Reynolds was guilty of no wrongdoing," Mr Dore added.
There are three investigations ongoing into the 'Prime Time Investigates' show that defamed Fr Reynolds.
RTE has made a full apology to him and last week agreed to pay him a substantial settlement.
Last night, a spokeswoman for Mr Shatter made it clear that he was no longer standing by the contents of his original statement on May 24 last.
She said that statement was based on an assumption that the matters detailed on the 'Prime Time Investigates' programme had been "fully researched and corroborated in accordance with proper journalistic and ethical standards".
"It is now known, of course, that with regard to Fr Reynolds, not only did he deny the allegations made but he also offered through his solicitor to engage in DNA testing and, despite said offer being made, the programme was broadcast," she said.
The spokeswoman said that Mr Shatter viewed this with the utmost seriousness and that he fully supported the Broadcasting Authority of Inquiry investigation ordered by the Government this week.
Mr Shatter has been at the centre of controversy about other comments made since being appointed minister last March.
He apologised to RTE crime correspondent Paul Reynolds last June for "unfair and inaccurate" remarks he made about him.
And last month, he dismissed criticisms by eight former attorneys general of the referendums on cutting judges' pay and Oireachtas inquiries as "nonsense" and "simply wrong".