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The president of Switzerland stepped to a podium in Bern in May and read a statement confirming rumors that had swirled through the capital for months. The government, he acknowledged, had indeed destroyed a huge 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 particular interest not only to Swiss prosecutors but to international atomic inspectors working to unwind 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 associations with Khan, acting as middlemen in his dealings with rogue nations seeking nuclear equipment and expertise.

The Swiss president, Pascal Couchepin, took no questions. But he 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.

Behind that official explanation, though, is a far more intriguing tale of spies, moles and the questionable 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 CIA.

Over four years, several of these officials said, operatives of the CIA paid the Tinners as much as $10 million, some of it delivered in a suitcase stuffed with cash. In return, the Tinners delivered a flow of secret information that helped end Libya’s bomb program, reveal Iran’s atomic labors and, ultimately, undo Khan’s nuclear black market.

In addition, U.S. and European officials said, the Tinners played an important role in a clandestine U.S. operation to funnel sabotaged nuclear equipment to Libya and Iran, a major but little-known element of the efforts to slow their nuclear progress.

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.