At the hearing in Washington DC, Judge Kennedy appeared to agree in part with the US government, saying at one point: "Why should the court not permit the department of Justice to do just that?"
The judge did not say when he would issue his ruling.
The hearing marked the first time the US government had been in court over the tapes since the CIA admitted earlier this month it had destroyed them.
David Remes, lawyer for the Guantanamo detainees, had asked the court to call an inquiry as the tapes - made in 2002 and not actually at Guantanamo - because they reportedly show two suspects undergoing waterboarding, a process of simulated drowning widely considered torture.
"We have a smoking gun, as it were, with respect to the government's destruction of potentially relevant evidence"
David Remes, US Guantanamo
Remes said the government was prohibited from destroying any evidence that could be relevant in a case, even if not directly noted in a court order.
"We have a smoking gun, as it were, with respect to the government's destruction of potentially relevant evidence," he said at the hearing.
However Joseph Hunt, the US justice department's lawyer, said a court inquiry would be "unwise and imprudent" and could damage the joint Justice Department-CIA investigation's investigation.
Hunt added that justice department officials would notify the court if they found evidence that Judge Kennedy's court order had been violated.
Remes countered that such an inquiry would be like "foxes guarding the henhouse".
In addition to the CIA-justice department investigation, both the US house and senate intelligence committees are holding inquiries into the scandal.
The CIA's admission earlier this month that the tapes had been destroyed caused widespread anger amongst human rights groups and some Democrat members of Congress.
The CIA denies torture and says the tapes were destroyed to protect the identity of the agents involved.