Minister for Justice Charlie Flanagan has told the Dáil that he "simply missed the significance" of the May 2015 email about the treatment of Maurice McCabe at the O’Higgins Commission.
Mr Flanagan was made aware of the email on 13 November this year, a full week before the Taoiseach was informed.
Former Tánaiste Frances Fitzgerald said she was informed on Thursday 16 November that it had been found in the department on 9 November.
The correspondence set out the legal strategy that was initially about to be pursued against Sgt McCabe at the O'Higgins Commission.
Mr Flanagan's comments came in the Dáil tonight as he apologised for his department's handling of the crisis and his conduct towards Labour TD Alan Kelly.
The minister apologised to the Taoiseach and the Dáil that information that was provided was subsequently proved to be inaccurate.
He said he was shocked that some documents had not been sent to the Disclosures Tribunal until this week.
"I was ... frankly horrified that there were records in the Department of Justice that should have been provided to the Disclosures Tribunal.
"As minister I have repeatedly emphasised the vital importance of full cooperation by the Department with the Tribunal."
He opened his statement with an apology to Mr Kelly for saying that the Labour TD was engaged in a smear campaign against him and withdrew his remarks.
Mr Flanagan said: "It is only right to acknowledge that Deputy Kelly's parliamentary questions should have been better handled by me."
Minister Charlie Flanagan apologises to Alan Kelly for saying that the Labour TD was engaged in a smear campaign against him pic.twitter.com/Srx3E541bI
— RTÉ News (@rtenews) November 28, 2017
The speech came after the resignation of Mr Flanagan's predecessor at the department for her role in the scandal.
It was also announced today that there would be an external inquiry into the workings of the Department of Justice, which would be completed before Christmas.
The department's secretary general Noel Waters, who had been due to retire in February, also said he was leaving the role today.
In a letter to staff, Mr Waters said that many of the claims in the media and in the Dáil about how the department had acted were not true.
He said it was a particularly difficult time for the department, but he was stepping aside entirely of his own volition.
Mr Waters said: "The department has been subject to a barrage of unwarranted criticism in recent days and most particularly today.
"I want to assure you that, in so far as is humanly possible, this department has sought at all times to act appropriately, upholding the law and the institutions of the State.
"Many of the claims about how the department has acted that have been made in the media and in the Dáil are not true, and I am confident that the processes that the Taoiseach has announced will show that to be the case."
However, in the Dáil tonight Mr Flanagan said the criticisms levelled at the department in recent days "are warranted".
He said he wanted to make sure that the events of recent days never happen again.
"I would like to say that there will be an investigation into the discovery of the documents, it will be independent, and it will be completed before Christmas," he said.
Earlier, the Taoiseach said the external inquiry at the department would examine the relationship between the department and gardaí.
Mr Varadkar said: "The events of the past few days have exposed major problems once again within a dysfunctional Department of Justice, including the way important emails were not found and therefore not sent on to the Charleton Tribunal during discovery.
"I am directing that there will be an external inquiry into that to report before Christmas. Systemic problems within the department were identified in the Toland Report.
"Minister Fitzgerald began the process of implementing the report, and this has continued under her successor Charlie Flanagan.
"These reforms will now be accelerated, and the Government is planning radical action to restore public confidence in the Department of Justice."
