NEW YORK - A US Central Intelligence Agency's deal with a family of Swiss engineers helped thwart the Libyan and Iranian nuclear programmes and undo Abdul Qadeer Khan's network, a leading American newspaper reported Monday. The New York Times, in a long story, said the operation involved Friedrich Tinner and his two sons, who have been accused in Switzerland of dealing with rogue nations seeking nuclear equipment and expertise. Over four years, the newspaper cited several unnamed officials as saying  that operatives of the C.I.A. 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 about Libya, Iran and Dr. Khan's network. In addition, American and European officials said, the Tinners played an important role in a clandestine American 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," Gary Samore, who ran the National Security Council's nonproliferation office when the operation began, was quoted as saying. "That's where we got the first indications that Iran had acquired centrifuges," which enrich uranium for nuclear fuel. Yet even as American officials describe the relationship as a major intelligence coup, The Times said compromises were made. Officials say the C.I.A. feared that a trial would not just reveal the Tinners' relationship with the United States " and perhaps raise questions about American dealings with atomic smugglers " but would also imperil efforts to recruit new spies at a time of grave concern over Iran's nuclear programme. 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 of the files. But in Europe, there is much consternation, according to the dispatch. "Analysts studying Dr. Khan's network worry that by destroying the files to prevent their spread, the Swiss government may have obscured the investigative trail. It is unclear who among Dr. Khan's customers " a list that is known to include Iran, Libya and North Korea but that may extend further " got the illicit material, much of it contained in easily transmitted electronic designs." On his part, Dr. Khan has denied any connection with the Swiss engineers when the story was first published quite some time ago. The report claimed Friedrich Tinner began working with Khan in the mid-1970s, using his expertise in vacuum technology to help Khan develop atomic centrifuges. But in 2000, the CIA recruited his son, Urs Tinner, who eventually persuaded his father and younger brother to join him as moles. As part of their services, the Swiss engineers helped the CIA sabotage atomic gear bound for Libya and Iran, the report said. In 2003 and 2004, inspectors from the International Atomic Energy Agency discovered vacuum pumps delivered to Iran and Libya that had been damaged cleverly so that they looked perfectly fine but failed to operate properly, according to The Times. They traced the defective parts from Pfeiffer Vacuum in Germany to the Los Alamos National Laboratory in the US state of New Mexico. In an interview with The Times, a senior European diplomat familiar with the I.A.E.A. said the destruction could have repercussions far beyond the case. For one thing, he said, the international atomic agency had been allowed to examine only parts of the archive. He called it "a good sample" and judged that the agency had missed no significant clues. Even so, he said, the agency might "come to regret" its inability to examine the materials further for insights into hidden remnants of Dr. Khan's network.