The recordings involved al-Qaeda suspects Abu Zubaydah and Abd al-Rahim al-Nashiri.
The justice department argued that the videos were not covered by the order because the two men were being held in secret CIA prisons overseas, not at the Guantanamo Bay prison.
Lawyers for a group of Guantanamo Bay inmates contesting their detention had requested the hearing to learn whether the government had complied with the preservation order.
They cited reports that information obtained from the interrogations implicated five unnamed Guantanamo detainees.
Detainee is strapped to a board and water is poured over face covered with cloth or cellophane
Sensation is akin to drowning, with reflexive choking, gagging and feelings of suffocation
Variations include dunking detainee headfirst into waterin Central and South America 30 years ago
Dates back to the Spanish Inquisition and used
Condemned by rights groups as torture
"We hope to establish a procedure to review the government's handling of evidence in our case ... and generally to require an accounting from a government that has admitted that it destroyed evidence," said David Remes, a lawyer for the group of inmates.
The CIA, pre-empting a news report, admitted on December 6 that it had destroyed hundreds of hours of interrogation tapes, prompting an outcry from congressional Democrats and human rights activists.
The tapes are believed to have shown interrogation methods that included simulated drowning known as waterboarding, which has been condemned as torture.
The CIA said it destroyed the tapes lawfully and did so out of concern for the safety of agents involved if the recordings were ever made public.
The White House has repeatedly denied that the US uses torture.
The justice department declined to comment on the judge's hearing order but the department last week urged Kennedy not to investigate the videotapes.
It also said that in light of other government probes into the tapes, a judicial inquiry into the destruction was inappropriate.
The government has also sought delays in congressional attempts to investigate the tapes' destruction, saying they would hamper a joint investigation by the justice department itself and the CIA.
"Plainly the government wants only foxes guarding this henhouse," Remes wrote in a court filing.