Malcolm Turnbull says Labor has launched a shameful attack on the integrity of the federal police and can't be trusted on national security.
Shadow attorney-general Mark Dreyfus says "concerns cannot help but arise" when a Labor frontbencher's office and an opposition staffer's home are raided by police in the second week of an election campaign.
Australian Federal Police officers executed search warrants on Senator Stephen Conroy's Melbourne office overnight as part of an investigation - requested by NBN Co - into the leaking of confidential national broadband network documents in December.
Commissioner Andrew Colvin defended his law enforcement agency after Labor challenged the government to say what it knew about the search operations in Melbourne two weeks into a close race between the major parties leading up to the July 2 federal election.
Documents seized during the raids had to be sealed after their holders claimed parliamentary privilege, meaning police are unlikely to be able to examine them for weeks.
"There has been no influence, no influence, on the AFP in the conduct of this investigation," Mr Colvin said on Friday.
NBN Co - the government owned builder of the national broadband network - had in December asked the AFP to investigate the leaking of confidential documents under a possible breach of commonwealth anti-disclosure laws.
Mr Colvin said the timing of the raids was determined by investigation's progress, and the fact that the leak had continued.
"We believe that the offending has been ongoing throughout," he said.
"The timing is completely determined by the AFP, it's determined by the status and the progress of the investigation, not by any external factors and not by any government influence."
The search of Senator Stephen Conroy's Melbourne office and the Brunswick home of a Labor staffer continued until 5am on Friday.
Officers also interviewed a number of people at NBN Co's headquarters in Sydney.
Attack on AFP's integrity a shameful thing to do: Turnbull
Mr Turnbull echoed the commissioner's comments when speaking to reporters in Launceston.
"The AFP made an independent decision to investigate it and ... undertake the various operational activities that they did yesterday," Mr Turnbull said.
"What Labor is doing is seeking to attack the integrity of the Australian Federal Police - that is a shameful thing to do.
"You can't trust Labor on national security."
The prime minister said he first became aware of the raids when notified by Justice Minister Michael Keenan on Thursday, after the minister had been briefed by the AFP chief.
Mr Dreyfus said it beggared belief that NBN Co had pursued the leaks without informing either the communications minister or the prime minister, who held the portfolio before becoming leader.
"It's absolutely vital that everybody understands that police forces do not act in a politically motivated manner," he said.
Treasurer Scott Morrison said the claim of a political stitch-up was a "pretty outrageous allegation".
The AFP will now need to get parliament's approval to look at the documents, which have been sealed under parliamentary privilege.
Mr Colvin said the timing of the raids on Thursday night was not determined by external factors but by the progress of the investigation.
Police were concerned "offending" had been going on while they were investigating, which was a key part of the reason for the timing of the raids.
The commissioner has asked the AFP's professional standards branch to look at whether the media were tipped off about the raids.
The incident has derailed the election campaigns of both major parties.
Mr Turnbull is campaigning in Tasmania to talk up the benefits of free trade deals for exporters.
Opposition Leader Bill Shorten is in western Sydney discussing Labor's plan to protect Medicare bulk-billing.
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