The Attorney-General's Department is confident it won't lose any more letters after the debacle involving correspondence from Sydney siege gunman Man Haron Monis.
Department secretary Chris Moraitis has conceded his staff may have been running around like "headless chooks" after it was revealed they had failed to give intelligence officials a letter Monis wrote to Attorney-General George Brandis asking if the preacher could contact Islamic State.
But they certainly weren't ducking for cover, he told a Senate inquiry hearing in Canberra on Monday.
"Mistakes have been made," he told the committee looking into why the letter also wasn't given to a high-level review into the response to the December 2014 siege.
Monis wrote the letter in October 2014.
Department officials initially told a Senate estimates hearing in late May that it had been passed on.
Four days later on June 1 they found that was not the case because the letter was included in a second tab of a spreadsheet.
"Why did it happen? I wish I knew the answer," Mr Moraitis said.
"Tab one, tab two, we've had this discussion hundreds of times."
On Monday it was revealed the second tab held all correspondence the department had since 2010 regarding Monis.
Mr Moraitis said he had wanted to be certain the letter hadn't been passed on in any way, including through conversations between his department and Prime Minister and Cabinet.
The secretary said he hadn't been aware PM&C had asked his department to correct the record on June 1.
Revelations of his department's mistakes had astounded him and he wanted to make sure the record was corrected properly.
"I had to also ensure that the department stopped making mistakes," he said.
His officials clarified the matter to parliament on June 4.
Labor senator Joe Ludwig asked how there could be any confidence in the way the department handled documents given what's come to light.
Mr Moraitis said there had been a lot of soul-searching about the department's processes.
But he denied any cover-up, saying the suggestion they'd been ducking for cover came from PM&C.
"Were we running around like headless chooks? Perhaps," Mr Moraitis said.
"But ducking for cover is not the language I would have used."
Deputy secretary Tony Sheehan said the case was a one-off human error rather than a systematic failure.
He told senators he was confident the department's new processes for handling documents had enough checks and balances to make sure a similar thing wouldn't happen again.
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