A family of Swiss engineers stands accused of helping smuggle nuclear technology. Centrifuge casings from Libya, under guard in Tennessee.

By WILLIAM J. BROAD and DAVID E. SANGER

The president of Switzerland stepped to a podium in Bern last May and read a statement. The government, he acknowledged, had destroyed a trove of computer files and other material documenting the business dealings of a family of Swiss engineers suspected of helping smuggle nuclear technology to Libya and Iran.
The files were of interest not only to Swiss prosecutors but to international atomic inspectors looking into the activities of Abdul Qadeer Khan, the Pakistani bomb pioneer-turned-nuclear black marketeer. The Swiss engineers, Friedrich Tinner and his two sons, were accused of having deep ties with Dr. Khan, acting as middlemen in his dealings with rogue nations seeking nuclear equipment and expertise.
The Swiss president, Pascal Couchepin, asserted that the files - which included an array of plans for nuclear arms and technologies, among them a highly sophisticated Pakistani bomb design - had been destroyed so that they would never fall into terrorist hands.
The real story is a far more intriguing tale of spies, moles and the compromises that governments make in the name of national security.
The United States had urged that the files be destroyed, according to interviews with five current and former Bush administration officials. The purpose, the officials said, was less to thwart terrorists than to hide evidence of a clandestine relationship between the Tinners and the C.I.A. Over four years, several of these officials said, operatives of the C.I.A. paid the Tinners as much as $10 million. In return, the Tinners delivered secret information that helped end Libya’s bomb program, reveal Iran’s atomic labors and, ultimately, undo Dr. Khan’s nuclear black market.
The relationship with the Tinners “was very significant,” said Gary S. Samore, who ran the National Security Council’s nonproliferation office when the operation began.
Destruction of the files, C.I.A. officials suspected, would undermine the case and could set their informants free. “We were very happy they were destroyed,” a senior intelligence official in Washington said .
European analysts studying Dr. Khan’s network worry that by destroying the files , the Swiss may have obscured the investigative trail.
The Swiss judge in charge of the Tinner case, Andreas Muller, said he had no warning of the planned destruction and is now trying to determine what, if anything, remains of the case against the Tinners.
As recounted in books and articles and reports by nuclear experts, Mr. Tinner worked with Dr. Khan for three decades, beginning in the mid-1970s. His expertise in vacuum technology aided Dr. Khan’s development of atomic centrifuges, which produced fuel for Pakistan’s nuclear arsenal, now estimated at 50 to 100 warheads.
Mr. Tinner’s involvement with Dr. Khan deepened in the late 1990s, when, joined by his sons, Urs and Marco, he helped supply centrifuges for Libya’s secret bomb program.
In 2000, American officials said, Urs Tinner was recruited by the C.I.A. Eventually, Urs Tinner persuaded his father and younger brother to join him as spies, and they began double lives, supplying Dr. Khan with precision manufacturing gear and helping run a centrifuge plant in Malaysia while cooperating with the United States.
Under growing pressure, Dr. Khan confessed. His clients turned out to include not only Libya but Iran and North Korea, and his collaborators turned out to be legion.
After the Tinners were arrested, Swiss and other European authorities began to scrutinize their confiscated files and to conduct wide inquiries. In 2005, Swiss authorities asked the United States for help in the Tinner case for more than a year. Washington ignored them.
“Its lack of assistance needlessly complicates this important investigation,” David Albright, of the Institute for Science and International Security, a private group in Washington, told Congress in May 2006.
In late July 2007, according to Swiss federal statements, the justice minister, Christoph Blocher, flew to Washington for talks with Mike McConnell, the director of national intelligence; Alberto R. Gonzales, then the attorney general; and Robert S. Mueller III, the F.B.I. director.
American officials discussed a range of possible outcomes with the Swiss and expressed their clear preferences. The best result, they said, would be turning over the family’s materials to the United States. Acceptable would be destroying them. Worst, according to the former administration official, would have been making them public in a criminal trial, where defense lawyers would have probably exposed as much American involvement as possible in hopes of absolving their clients.
Last March, Mr. Muller became the examining magistrate in the Tinner case, charged with assessing if a trial was warranted. Soon after, he was quoted as saying the evidence contained “obvious holes.” Then, on May 23, the Swiss president, Mr. Couchepin, revealed that Switzerland had begun a series of extraordinary actions just days after Mr. Blocher, the justice minister, returned from Washington.
Swiss citizens are prohibited from aiding foreign spies. But in his statement, the president said that in late August 2007, the government canceled a criminal case against the Tinners for suspicions of aiding a foreign government. Though unmentioned, the C.I.A. seemed to be part of the story.
On November 14, his statement continued, the government decided to destroy “the comprehensive holding of the electronic files and documents” seized from the Tinners. The most dangerous items, the president said, included “detailed construction plans for nuclear weapons, for gas ultracentrifuges for the enrichment of weapons-grade uranium, as well as for guided missile delivery systems.” International atomic inspectors, he added, supervised the destruction.
Mr. Couchepin said keeping the documents “was incompatible with Switzerland’s obligations” under the Nuclear Nonproliferation Treaty and added, “Under all circumstances, this information was not to reach the hands of a terrorist organization or an unauthorized state.”
The statement provoked a political furor. Some politicians and columnists accused Switzerland of surrendering to Washington’s agenda and violating Swiss neutrality. Among the strongest critics was Dick Marty, a prominent Swiss senator. “We could have respected the treaty by avoiding their publication and putting them under lock and key,” he was quoted as saying on Swissinfo, the Web site of the Swiss Broadcasting Corporation. Destroying them, he added, “could lead to the collapse of the legal case.”
Many European officials dismissed the government’s arguments about terrorists and rogue states .
“If they had kept the material in federal possession for years, why not keep holding it-” asked Victor Mauer, a senior official at the Center for Security Studies of the Swiss Federal Institute of Technology. “Their explanation is not convincing.”