A seven-year effort by the Central Intelligence Agency to hide its relationship with a Swiss family who once acted as moles inside the world’s most successful atomic black market hit a turning point on Thursday when a Swiss magistrate recommended charging the men with trafficking in technology and information for making nuclear arms.

The prospect of a prosecution, and a public trial, threatens to expose some of the C.I.A.’s deepest secrets if defense lawyers try to protect their clients by revealing how they operated on the agency’s behalf. It could also tarnish what the Bush administration once hailed as a resounding victory in breaking up the nuclear arms network by laying bare how much of it remained intact.

“It’s like a puzzle,” Andreas Müller, the Swiss magistrate, said at a news conference in Bern on Thursday. “If you put the puzzle together you get the whole picture.”

The three men  Friedrich Tinner and his two sons, Urs and Marco  helped run the atomic smuggling ring of A. Q. Khan, an architect of Pakistan’s nuclear bomb program, officials in several countries have said. In return for millions of dollars, according to former Bush administration officials, the Tinners secretly worked for the C.I.A. as well, not only providing information about the Khan network’s manufacturing and sales efforts, which stretched from Iran to Libya to North Korea, but also helping the agency introduce flaws into the equipment sent to some of those countries.