The cabinet has strongly criticised the publication of a secret document on alleged CIA prisons in eastern Europe.
It said the publication of the classified document in the mass-circulation Sunday newspaper, SonntagsBlick, had damaged the credibility of the country.
A government spokesman said the fax in question intercepted by the Swiss intelligence services included information that was already known publicly but which had yet to be verified.
He refused to give any more details, beyond saying that the cabinet had condemned the leak to the press.
Justice Minister Christoph Blocher said he supported transparency but added that secret documents should remain classified.
On Sunday the newspaper made the intercepted document public, saying the fax was received by the Egyptian embassy in London and that it supposedly confirmed the existence of detention centres.
The message was picked up by the secret service's Onyx satellite listening system on November 10, just three days after the Council of Europe launched its investigation into allegations that the CIA has been running secret interrogation centres in Europe.
The Egyptian fax stated that 23 Iraqi and Afghan citizens had been transferred to a Romanian military base near the port of Constanza for interrogation purposes. It added that similar detention centres had been set up in Ukraine, Kosovo, Macedonia and Bulgaria.
Ueli Leuenberger, a Green Party member of parliament and expert on human rights, criticised the government's failure to act on the intelligence.
"The information should have been handed over to Dick Marty [Swiss head of a Council of Europe investigation into the alleged prisons]," Leuenberger told swissinfo.
"The government should also have issued a formal protest to the United States government. It's precisely because the cabinet didn't act that the leak occurred.
"These [CIA] violations only encourage those who disregard international law," he added.
Marty told French-language radio that he "regretted that the occasion was not seized to deplore the use in Europe of undercover methods to combat terrorism".
"We don't hesitate to criticise human rights abuses when they take place in Cuba, Tunisia or Myanmar," he continued.
"But when it comes to a powerful ally, we are so careful that it borders on subservience."
The Federal Prosecutor's Office and military prosecutors are investigating a possible breach of official secrets by the SonntagsBlick editor as well as two journalists at the newspaper.
Publishing a secret document can be a violation of Swiss law punishable by a fine or imprisonment.
swissinfo with agencies
On Sunday the Swiss paper SonntagsBlick published a confidential fax sent by Egypt's foreign ministry to the Egyptian embassy in London, intercepted by the Swiss intelligence service in November, confirming the existence of secret prisons in Europe.
Swiss politicians fear the affair will discredit the Swiss intelligence agencies and on Tuesday a parliamentary sub-committee called on the government to act.
On Monday military prosecutors in Switzerland opened an investigation into a newspaper editor and two journalists, suspected of publishing military secrets.
June 2004: Human Rights Watch claims that the United States is detaining alleged terrorists at more than a dozen secret locations around the world.
November 2, 2005: The Washington Post reports that the CIA is detaining members of al-Qaeda in eight eastern European countries and Asia.
November 7: Swiss parliamentarian Dick Marty is appointed head of a Council of Europe inquiry into the allegations.
December 8: The American secretary of state, Condoleezza Rice, refuses to answer questions on the subject during a tour of Europe.
December 14: The Swiss parliament demands a report from the government on alleged CIA transit flights in Swiss airspace.
January 8, 2006: The SonntagsBlick newspaper claims to have received a copy of a fax from the Egyptian government confirming the detention centres.