Judge Peter Smithwick accused the minister of “interfering” with the independence of his tribunal and causing major witnesses to reconsider giving evidence to it.
In a series of terse letters, the judge insisted Mr Shatter’s imposition of a deadline on the probe threatened the entire investigation.
Among witnesses now reconsidering co-operation with the tribunal was one from outside the state whose involvement with the probe took some time to secure, according to the judge.
The outspoken attack on Mr Shatter was seized on by the opposition, which accused the minister of threatening the validity of the probe.
Mr Shatter pushed through an Oireachtas motion soon after the general election imposing a November deadline on the tribunal, which is probing allegations of Garda collusion in the IRA killings of Superintendent Bob Buchanan and Chief Superintendent Harry Breen near the border after a meeting at Dundalk Garda Station in March 1989.
Mr Shatter rejected the judge’s claims, insisted he was trying to bring “transparency” into the tribunal situation, and pointed out that the hearings had cost taxpayers €8 million since it was created in May 2005.
Judge Smithwick branded the minister’s move a “wholly inappropriate” bid to “interfere with the independence” of the inquiry.
The judge also condemned “spin” surrounding a Government statement on the curtailment of the tribunal.
“This was done without any prior notice to me or communication whatever. I think this was singularly ill-advised,” he said.
The letters, released through the Oireachtas, show Judge Smithwick was very concerned the tribunal would be compromised by the imposition of the deadline. The tribunal chairman said the chain of events would aid those who wanted to frustrate the probe as they would know they only had to withhold co-operation for another few months.
Judge Smithwick also warned the deadline would help discourage sensitive and important witnesses from outside Ireland coming forward because they would see the inquiry as being wound down.
The judge remarked that he had a duty to protect people’s lives and allow those whose reputations are being risked by the evidence being heard the opportunity to defend their good name.
Fianna Fáil justice spokesman Dara Calleary said the minister’s stance could have dire consequences. “By wading into the tribunal’s work, just as it reached its critical phase, Mr Shatter threatens public acceptance of the tribunal’s independence and risks undermining the entire point of this expensive but crucial initiative.”