The plaintiffs say the government investigations are needlessly intrusive and violate their privacy rights. They suggested that the federal government should have learned something from how it treated an earlier generation of scientists, including J. Robert Oppenheimer, who led the effort to develop the atomic bomb during World War II and was later stripped of his security clearance in the McCarthy era.

“We see history repeating itself,” Dr. Nelson said. “These guys went to leftist meetings in the ’30s, did heroic science in the ’40s and were persecuted in the ’50s.”

Dr. Nelson, who has been with the laboratory for 30 years, works on the Cassini mission, which involves a spacecraft orbiting Saturn. He and other plaintiffs do not have security clearances and are not involved in classified or military activities.

Zareh Gorjian, another plaintiff, told my colleague Andrew C. Revkin that he could not understand what the government was after. “I was at J.P.L. during the cold war when we were fighting the Soviet Union, which had the power not only to end all life in the U.S. but the entire planet,” Mr. Gorjian said. “We were able to defeat them without resorting to such intrusive tactics.”

The Ninth Circuit provisionally agreed with the plaintiffs, saying they had raised serious questions about their privacy rights. A three-judge panel of the court ordered the background checks halted while their case goes forward.

When the full court was asked to hear the case, its judges were sharply divided over whether the investigations were routine or troublesome.

Judge Andrew J. Kleinfeld, in a second dissent, said the court’s decision “is likely to impair national security” by forbidding the government “from doing what any sensible private employer would do.” He mentioned espresso stands and clothing stores, adding, “Most of us do not hire law clerks and secretaries without talking to professors and past employers.”