Smuggling charges should be brought against three Swiss engineers suspected of giving nuclear weapons technology to a rogue network in Pakistan, a magistrate said on Thursday, in a case involving CIA ties, shredded documents and national security implications.

Investigating magistrate Andreas Mueller said his recommendation that the trio, two brothers and a father, face trial is based on an exhaustive probe into an alleged nuclear smuggling ring. Mr. Mueller submitted his confidential report to federal prosecutors, who will decide whether to bring charges on violating Swiss nonproliferation laws.

Mr. Mueller oversaw the last three years of a six-year federal probe against Urs Tinner, his brother Marco and their father Friedrich. The politically sensitive case was slowed down after the Swiss government repeatedly ordered evidence destroyed in the case, allegedly under pressure from senior U.S. officials.

The Tinners are suspected of links to the nuclear smuggling network of Abdul Qadeer Khan, the creator of Pakistan’s atomic bomb. They allegedly supplied Khan’s black market nuclear network with the technical expertise and equipment used to make gas centrifuges. Khan sold the centrifuges for secret nuclear weapons programs in countries that included Libya and Iran before his operation was disrupted in 2003.

Mr. Mueller, who said he is relieved to be done with the investigation, harshly criticized the Swiss government for having “massively interfered in the wheels of justice by destroying almost all the evidence.” He said the government also ordered federal criminal police not to cooperate with him.

“There are many parts. It’s like a puzzle and if you put the puzzle together you get the whole picture,” Mr. Mueller said at a news conference. “There is not (just) one piece of evidence, there are many pieces of evidence.”

U.S. officials in Bern had no immediate comment.

Mr. Mueller said he recommended the three face charges for “supporting the development of atomic weapons” in violation of nonproliferation laws, while Marco Tinner should face additional charges of money laundering.

Mr. Mueller’s 174-page report “is now being studied in detail” by the Swiss attorney general’s office, which “will inform the public in due course” on whether charges will be filed against the Tinners, Federal Prosecutors Office spokeswoman Jeannette Balmer said.

Mr. Mueller said the Tinners did not deny working for the A.Q. Khan network, but claimed they did not know his aim was to produce nuclear weapons. He also said the Tinners had worked for the CIA since June 2003.

“The findings are that the Tinners might be part of the Khan network,” Mr. Mueller told The Associated Press after the news conference.

“And beginning where they should have known that Khan produced atomic weapons, in May 1998, until they started to collaborate with the secret services, in June 2003, they in their specific roles were part of this network, and delivered parts to the network that the network then itself delivered to other countries, (such) as Libya,” Mr. Mueller said.

He told AP that “there is no contrary proof that they were not on the payroll” of the CIA.

In June 2009, the Swiss government ordered the destruction of about 100 pages of evidence linked to Mr. Mueller’s investigation of the Tinner family, saying they contained information that could have endangered national security and needed to be kept out of “the wrong hands.”

The Cabinet, or Federal Council, said those documents were “the most explosive” material in the case’s file of more than 1,000 pages.

Copies of some of the shredded files have reportedly resurfaced, however, and could form part of the case against the Tinners, who have repeatedly maintained they are innocent.

The documents are copies of files destroyed in 2007 under a previous order that led to protests from lawmakers and legal experts, who said the government had undermined the prosecution in the smuggling case. The copies were found in prosecutors’ archives in December 2008.

Less sensitive documents, such as those dealing with uranium enrichment, were ordered kept under high security at the Federal Justice Department. The government said investigators, prosecutors, courts and the Tinner family’s lawyers would be able to view them under tight restrictions, but the documents would be destroyed at the end of legal proceedings.

A report this week by a Washington-based think tank found the Swiss authorities, the CIA and the Tinners were all responsible for failing to limit the spread of nuclear weapon technology and know-how.

The Institute for Science and International Security’s report particularly pointed blame at Swiss justice and U.S. intelligence officials for their failure to cooperate. It also says the Tinners persuaded businesses to make parts for machines without knowing their true purpose.

Mr. Mueller said the shredding of files had complicated an already complex case and made it harder to piece together a complete picture of the Tinners’ alleged involvement in the Khan ring. Switzerland’s highest criminal court has criticized the government for opting to destroy further evidence and said it was disappointed not to be informed earlier.

Complicating the case further are claims by Urs Tinner that he supplied the CIA with information that led to the breakup of Khan’s network. In a recent documentary, Tinner told Swiss TV he tipped off U.S. intelligence about a delivery of centrifuge parts meant for Libya.

The shipment was seized at the Italian port of Taranto in 2003, forcing Libya to admit and eventually renounce its efforts to acquire nuclear weapons.

Former Swiss Justice Minister Christoph Blocher said the government decided to destroy the original documents after he refused in 2007 an American request to hand over thousands of the files.

Urs Tinner was released in December 2008 after almost five years in investigative detention and has yet to be charged. A Swiss parliamentary panel has investigated the government-ordered shredding of thousands of files of evidence in the case

The Khan network was disrupted when Western intelligence agencies intercepted the centrifuge parts meant for Libya’s nuclear weapons programme.

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