Barry H. Stern, an aide to Attorney General Dick Thornburgh for more than a decade, is resigning his post as associate deputy attorney general, continuing a recent exodus of high-level officials from the Justice Department.

Stern said his departure -- to take a job as lawyer for a magazine and newsletter publishing company near Philadelphia -- is unrelated to the personnnel problems that have shaken the department in the past two months.

"I've been hoping to leave for the past year," said Stern, 43. "I've been living out of a hotel room since last December and commuting to Philadelphia."

Administration officials described the resignation as a further sign of the break-up of Thornburgh's "inner circle" -- a small group of aides and political advisers who served under him when he was governor of Pennsylvania and then came to Washington when he became attorney general in August 1988.

It also ends a long-running dispute between Stern and Justice Department security officials over his failure to complete a security clearance questionnaire -- a dispute that one administration official said raised questions about the adequacy of Justice security procedures.

When Stern joined Justice in September 1988 as director of the office of liaison services, he and other top Thornburgh aides received temporary security waivers, pending an FBI background check, that gave them access to sensitive department information. Last November, Stern was named by Thornburgh to his current post, where he oversaw the department's funding for its organized crime drug enforcement task forces and its program to seize and distribute the assets of drug dealers and other criminal suspects.

Stern said he initially filled out the security form, known as Standard Form 86, Questionnaire for Sensitive Positions, in the summer of 1989. But last November, the Office of Justice Security Programs sent back the form, saying the FBI could not begin its background check because he had failed to give complete information on a number of routine questions, such as his employment activites after graduating from law school and the addresses of two references.

Stern confirmed that he never responded to the security office's request to complete the form. "They called me a couple of times about it, and I said, okay, okay, okay, then I forgot about it," Stern said. "But I knew I was leaving by then."

Stern said that he did not routinely see sensitive national security or law enforcement information on his job. But one administration official familiar with the matter said it was "highly irregular" for an official to have access to sensitive material for that long without an FBI background check. Sources confirmed that it became a source of irritation between Stern and department security officials.

Stern's decision to leave makes him the fourth senior Justice official to resign in the past two months. In May, Deputy Attorney General Donald B. Ayer and his top deputy, Peter A. Nowinski, abruptly quit following a series of disputes between Ayer and Thornburgh. Edward S.G. Dennis Jr., chief of the criminal division, announced he was leaving last month to take a job with a Philadelphia law firm.

Stern's ties to Thornburgh go back to 1978, when he worked on the attorney general's first campaign for governor; he later served as Thornburgh's state secretary of labor and industry.

A department spokesman said yesterday that Thornburgh "wishes him well" in the private sector, adding, "He understood all along that Barry was more committed to being in Philadelphia than in Washington."