Justice Department lawyers, in a response Friday with the U.S. District Court in San Francisco, also argued that Judge Vaughn Walker had no cause to penalize the government over its refusal to turn over the document.
Walker on May 22 threatened to punish the administration for withholding the document, which he ordered given to lawyers suing the government over its warrantless wiretapping program.
The judge has ordered department lawyers to appear before his court Wednesday to make the case why he should not award damages to the now-defunct Oregon chapter of the Al-Haramain Islamic Foundation. That group is challenging the wiretapping program.
In its response, the department said that in this case "disclosure of classified information - even under protective order - would create intolerable risks to national security."
The filing said President Barack Obama has authorized access to classified information on a "need-to-know" basis and argued that the government "cannot be sanctioned for its determination that plaintiffs do not have a need to know classified information."
The Al-Haramain case has been a focal point for civil liberties groups questioning the legality of the warrantless wiretapping program, and has become one of several instances where the current administration has taken its cue from the Bush administration in citing national security as justification for keeping secrets.
Attorney General Eric Holder has ordered a review of all state secrets used by the Bush administration to protect anti-terrorism programs from lawsuits.
But the Obama administration is also fighting the court-ordered release of prisoner-abuse photos and is reviving, in a revised form, military tribunals where suspected terrorists have limited access to information.
The Bush administration inadvertently turned over the top secret document to Al-Haramain lawyers, who claimed it proved illegal wiretapping by the National Security Agency.
The document was returned to the government, and the lawyers have argued they need the document back to prove their case.
The Treasury Department in 2004 designated the charity as an organization that supports terrorism.
By Associated Press Writer Jim Abrams