The Justice Department and Naval Investigative Service (NIS) are investigating alleged errors and wrongdoing by Navy probers in San Diego, including apparent failure to pursue evidence that a classified computer disk was stolen, two congressional offices have reported.

The probes grew out of controversy surrounding Stephen S. Stokwitz, an award-winning civilian Navy attorney dismissed from his $52,500-a-year post at a San Diego research facility in 1984.

Stokwitz has become the focus of efforts to grant new job protection to more than 1 million "excepted service" federal employes, including lawyers, who can be dismissed without cause or a chance to question their accusers.

NIS agent Winston Kuehl said agents did not follow up Stokwitz's report about a stolen computer disk because federal attorneys said Stokwitz should not be granted confidentiality, as he had requested, while he had a suit pending against several government officials.

Kuehl said Stokwitz's attorney also indicated that information on the disk did not compromise national security.

NIS documents recently released to Stokwitz's attorneys show that the investigators failed to persuade federal prosecutors that allegations of drug abuse and financial misconduct against Stokwitz would stand up in criminal court.

The investigators kept the inquiry alive an additional year in order to examine Stokwitz's bank accounts before prosecutors concluded that the case "lacks prosecutive merit," the NIS report said.

Rep. Jim Bates (D-Calif.), whose inquiry about the missing disk sparked a top-level NIS investigation, said the Stokwitz case is one of many indicating that the NIS "is really incompetent." He has asked that the unit be disbanded.

An aide to Rep. Mervyn M. Dymally (D-Calif.), who has cited the case in attacking the "excepted service" system, has told Stokwitz that the Justice Department has agreed to look into charges that the Navy improperly reviewed his tax returns and made "sexual" movies of him with a woman.

Stokwitz, 34, was discharged as general counsel of the Naval Ocean Systems Center shortly after being recommended for promotion. According to Navy documents, the dismissal grew out of allegations, never formally lodged, that he had coerced employes to lend him money, cheated on a travel voucher, had sex in his office and used cocaine.

Stokwitz said he had frequently reprimanded two employes who made the charges because they had made mistakes in their work. He has sued them, naval investigators who pursued the charges and other officials for $1 million in damages.

The most recent probe of NIS procedures began after another NOSC employe, expressing sympathy for Stokwitz, told him that she had evidence of other misdeeds and lax security at the center. She showed him what appeared to be a computer disk with classified information that she said she had taken from the office to prove her point.

Stokwitz said that he advised her to return the disk and that his attorney, Nathaniel P. Ward IV of San Diego, accepted a one-page printout of information on the disk to show to investigators.

Ward said he notified NIS headquarters in October of the possible theft. Even after being told about "hard-copy evidence of the theft of the disk," Stokwitz said, "the Navy did not even interview me despite the fact that to this day I still am holding the documentary evidence."

Assistant U.S. Attorney John Neece, defending the government in Stokwitz's suit, said he advised the NIS not to interview Stokwitz if his statements could not be used.

Stokwitz, celebrating the U.S. attorney's decision to drop its criminal investigation, said he thinks it significant that after several official investigations, including surveillance of his house and a look at his tax returns, "not one charge could be supported or warranted."