Lawyers acting for Megaupload have accused the United States Justice Department of intentionally misleading a US court when applying for a search warrant that it later used to seize and take down the file-sharing service.

Megaupload said in a submission today to the US Federal Court in Virginia that the Justice Department had claimed Megaupload had failed to remove 36 pirated movies from its servers for more than a year, when it knew all along that the company was actually co-operating in a secret criminal investigation over the offending content.

Ira Rothken, the lawyer leading Megaupload's defence, tweeted that the US government had "intentionally misled" the court in order to take down Megaupload.

The fact Megaupload had left the copyright-infringing movies on its servers between June 2010 and November 2011 was the only "direct, corroborated evidence" the Justice Department gave the court of criminal complicity by Megaupload, Rothken said in a blog post.

The affidavits the department provided to obtain the search warrant suggested Megaupload was a "brazen scofflaw" that persisted in hosting the files without concern for their illegal content, he said.

"The truth, as the Government well knows, is quite different.

"Megaupload had every reason to retain those files in good faith because the Government had sought and obtained Megaupload's cooperation in retrieving the files and warned that alerting users to ... the Government's interest in the files could compromise the investigation," he said.

Megaupload's lawyers said Megaupload had voluntarily arranged for its hosting company, Carpathia - which had been acting as a go-between in the investigation - to supply the Government with the pirated movies, as requested.

They produced a June 2010 email from Carpathia business director Phil Hedlund to Kim Dotcom, in which Hedlund promised to convey Megaupload's assistance in relation to the investigation to the US government.

The court ordered the search warrant application be released in November following an approach by Kyle Goodwin, a Megaupload user who is trying to get back access to files he had uploaded to the file-sharing site.

Megaupload's lawyers said the US government's "misleading" actions called into question the validity of the search warrants and was "all the more worrisome considering the identified pattern of governmental misconduct plaguing the proceedings in New Zealand".

Megaupload founder Kim Dotcom, who is still battling extradition to the US, is due to unveil his new file-sharing service, mega.co.nz, at his Auckland mansion on January 20.