The Obama administration has asked a secret surveillance court to ignore a federal court that found bulk surveillance illegal and to once again grant the National Security Agency the power to collect the phone records of millions of Americans for six months.

The legal request, filed nearly four hours after Barack Obama vowed to sign a new law banning precisely the bulk collection he asks the secret court to approve, also suggests that the administration may not necessarily comply with any potential court order demanding that the collection stop.

US officials confirmed last week that they would ask the Foreign Intelligence Surveillance court – better known as the Fisa court, a panel that meets in secret as a step in the surveillance process and thus far has only ever had the government argue before it – to turn the domestic bulk collection spigot back on.

Justice Department national security chief John A Carlin cited a six-month transition period provided in the USA Freedom Act – passed by the Senate last week to ban the bulk collection – as a reason to permit an “orderly transition” of the NSA’s domestic dragnet. Carlin did not address whether the transition clause of the Freedom Act still applies now that a congressional deadlock meant the program shut down on 31 May.

But Carlin asked the Fisa court to set aside a landmark declaration by the second circuit court of appeals. Decided on 7 May, the appeals court ruled that the government had erroneously interpreted the Patriot Act’s authorization of data collection as “relevant” to an ongoing investigation to permit bulk collection.

Carlin, in his filing, wrote that the Patriot Act provision remained “in effect” during the transition period.

“This court may certainly consider ACLU v Clapper as part of its evaluation of the government’s application, but second circuit rulings do not constitute controlling precedent for this court,” Carlin wrote in the 2 June application. Instead, the government asked the court to rely on its own body of once-secret precedent stretching back to 2006, which Carlin called “the better interpretation of the statute”.

The second circuit court of appeals is supposed to bind only the circuit’s lower courts. But the unique nature of the Fisa court – whose rulings practically never became public before whistleblower Edward Snowden’s revelations – has left ambiguous which public court precedents it is obliged to follow.

“While the Fisa court isn’t formally bound by the second circuit’s ruling, it will certainly have to grapple with the second circuit’s interpretation of the ‘relevance’ requirement. The [court] will also have to consider whether Congress effectively adopted the second circuit’s interpretation of the relevance requirement when it passed the USA Freedom Act,” said Jameel Jaffer, the deputy legal director of the ACLU, which brought the lawsuit the second circuit decided.

The second circuit did not issue an injunction stopping the bulk collection. It deferred to the then-ongoing congressional debate over the USA Freedom Act, citing legislation as the more appropriate mode of relief. The ACLU, now confronting a potential return of bulk surveillance via the Fisa court, is considering seeking an injunction in the appropriate federal district court should the Fisa Court grant the government surveillance request.

Yet Carlin’s request to the Fisa court suggested the Obama administration would not consider the second circuit the last word – and might seek to challenge the injunction.

Carlin told the Fisa court that the government was “considering its litigation options in regard to the second circuit’s opinion”, which would have to mean a challenge before the US supreme court.

Carlin added in a footnote: “In the event an injunction of some sort were to issue by the district court, the government would need to assess, in light of the nature and scope of whatever injunction the district court issued, its ability to carry out authority granted under an order issued by this court.”

But the Fisa court must first decide whether the new bulk-surveillance request is lawful.

On Friday, the conservative group FreedomWorks filed a rare motion before the Fisa court, asking it to reject the government’s surveillance request as a violation of the fourth amendment’s prohibition on unreasonable searches and seizures. Fisa court judge Michael Moseman gave the justice department until this coming Friday to respond – and explicitly barred the government from arguing that FreedomWorks lacks the standing to petition the secret court.

“The only federal appeals court to have considered this surveillance concluded, after very careful analysis, that it’s unlawful. It’s disturbing and disappointing that the government is proposing to continue it,” said Jaffer, of the ACLU.