The "missing" files on the 1969 arms crisis were found by staff of the National Archives yesterday. The Government Press Office confirmed that the files, Partition - Government Policy, were found in the archives yesterday morning where they had been transferred from the Department of the Taoiseach in 1996 for "safekeeping".
They were not released for public inspection in 1996 as they were not yet 30 years old.
The discovery of the files followed two days of controversy after the chairwoman of the National Archives Advisory council, Ms Margaret MacCurtain, said they were missing and an investigation into their whereabouts would be instigated.
The Fine Gael leader, Mr John Bruton, called on the Taoiseach to initiate a Garda inquiry into the missing documents on the arms-smuggling scandal, which led to the sacking of Mr Charles Haughey and Mr Neil Blaney from government in 1970.
A Government spokesman said last night the files would be examined to determine if they can be released for public inspection under the 30-year rule.
The examination would be complete within days.
The director of the National Archives, Dr David Craig, said yesterday he was "embarrassed and sorry for any inadvertent misleading of the public" about the files.
"I am extremely glad the files have been found. It was a great relief they have not been lost."
Dr Craig said the files covered the period September 1968 to November 1969, including August 1969.
There are six files, contained in two boxes, plus an annexe to one of the files.
Dr Craig said the files all related to partition. "They are Department of the Taoiseach files from the time which became, in effect, the main file on Northern Ireland," he said. They include briefings to the government of the time, but do not include anything that would have gone directly to the minister for justice, he said.
The papers constitute a couple of thousand sheets of paper. A Government spokesman said last night that as soon as they were returned to the Department of the Taoiseach yesterday, an official from the Northern Ireland Division started to go through them.
The files have to be inspected before their release to ensure they do not contain information that would endanger national security.
Mr Bruton last night accused the Taoiseach's office of being "very sloppy" in the checking of its 1969 files last year in preparation for public release.
"Under the Act, all files had to be individually checked so any gap in the files should have been immediately obvious even to a casual reader," he said.
Mr Bruton said the Taoiseach's office had the use of the most advanced IT and operated under what it called a system of strategic management.
"So how did it manage such a cock-up?"
He said the National Archives Office also had questions to answer about what it did with the materials it got in 1996.
Mr Bruton said he would still be raising the issue with the Taoiseach when the Dail resumed at the end of the month.
The Dublin Fianna Fail TD, Mr Pat Carey, last night called on Mr Bruton to apologise for what he said were "outrageous" comments on the missing papers.
"It is Mr Bruton who has displayed sloppiness and undue haste in his reaction to weekend media reports on the issue and who should now be severely embarrassed by the facts that have been established, and not the Taoiseach's office as Deputy Bruton claimed," Mr Carey said.
He said it was now clear that no one was involved in "trying to rewrite history" or cover up something by attempting to remove or destroy files, as Mr Bruton had claimed.
The former president of the Workers' Party, Mr Tomas MacGiolla, welcomed the discovery of the papers but warned the Government against concealing key historical documents. He said all the material must be released.
"This was a key period during which the ground was laid for all that would happen over the coming three decades.
"Unless all of the relevant papers for this period are released there will continue to be a justifiable suspicion of deliberate tampering with the files and with history itself."