LOS ANGELES, OCT. 22 -- A scheme to sell the Soviet Union plans for a highly advanced supercomputer with military applications was thwarted today with the arrest of three men in the San Francisco Bay area, federal officials and a computer company spokesman said.

Rollin Klink, special agent in charge of the U.S. Customs Service northern California and Nevada district, said a Defense Department assessment of the stolen plans indicated that this was "the most significant case U.S. Customs has worked on."

Klink said the matrix processing supercomputer developed in California's Silicon Valley would have allowed the Soviets "to anticipate American missile strikes, track American submarines and intercept American communications."

Federal officials and a spokesman for the Saxpy Computer Corp., the device's manufacturer, said former Saxpy software engineer Ivan-Pierre Batinic, 29, of Fremont, Calif., his brother, Stevan, and software designer Kevin Anderson, 36, also of Fremont, were arrested at separate Bay Area locations and arraigned late today before a federal magistrate in San Jose.

Officials charged that the three cooperated in a conspiracy to violate U.S. export controls and transport stolen goods with Charles McVey, 57, a one-time fugitive indicted for export violations in 1984 and now held in a Canadian jail.

Federal officials said plans for the computer -- along with tapes, floppy disks and manuals -- were recovered today from a storage locker Anderson had rented in Fremont. They said their investigation began in August when Ivan-Pierre Batinic and Anderson were stopped briefly by customs agents on their return from Canada and were found to have $10,000 in $100 bills.

Before being fined and sent on their way, they told customs agents that the money came from a man named Carlos William Beltran, Klink said. That was the name on a Guatemalan passport carried by McVey when he was arrested by Canadian officials shortly thereafter. At the time of his arrest, McVey carried a Saxpy equipment manual.

Sandy Towle, director of market development for the Sunnyvale-based company, said the tapes and blueprints stolen from the plant provided "the soul" of the computer and were valued at $1.9 million. Federal agents said the men planned to sell them to the Soviet Union for $4 million. One official said he had information that one of the men had traveled to Moscow.

Towle said Ivan-Pierre Batinic, reportedly a French citizen, did not have a security clearance and did not need one because Saxpy has no government contracts. Federal officials said the stolen plans were not classified, but could not be exported without government permission.

Towle acknowledged that such a high-speed computer might be useful in any U.S. missile defense "Star Wars" system. He said that the computer represented "the next evolutionary step in the high-speed processing of data," but that so far the U.S. government had not indicated interest in buying it.

"We would be delighted" to sell it to the government, Towle said.

Towle said the company announced the development of the supercomputer May 5 and that Saxpy officials had been asked by FBI and customs agents to cooperate in an investigation of a plot to steal vital information about the computer.

Batinic joined the company June 20, 1986, and resigned last month, indicating he had found another job. Towle said the stolen material recovered today amounted to "a couple reels of tape and some blueprints" that would show how to build the circuits and software for the 3,800-pound device.