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The FBI's background investigation of defense secretary-designate John Tower has uncovered extensive government files depicting repeated security violations at a sensitive U.S. diplomatic mission in Geneva during Tower's tenure there as a chief arms-reduction negotiator.

In the midst of an extensive Pentagon investigation of Geneva security breaches, the files show, Tower and other U.S. negotiators wrote memos in 1986 strongly defending an Air Force colonel who was a chief target of the security investigation. A State Department security official later suggested that the officials' support for the colonel, who subsequently was reprimanded for sexual misconduct, "may have been influenced" by assistance he has given them "in personal and professional matters . . . some of which bordered on improper conduct."While the files examined by Newsday are sprinkled with references to Tower, they appear to contain no substantiated evidence that he personally was involved in security lapses. However, they paint a startling picture of questionable conduct by U.S. diplomatic, military and intelligence personnel assigned to conduct critical negotiations with the Soviet Union on such issues as the Strategic Defense Initiative and nuclear arsenal reductions.

The thousands of pages of documents, some stamped "secret," focus heavily on the statements of a now-retired Air Force colonel, Robert L. Moser Jr., but also cover broader security problems. The documents cite, for example:

-Moser's recitation of sexual liaisons involving at least a dozen unnamed U.S. personnel then assigned to the Geneva mission, sometimes with foreign nationals.

-Repeated instances of heavy drinking and unauthorized contacts with Soviet representatives by U.S. personnel in Geneva at such "KGB hangouts" as the Pickwick Pub and Jimmy's Bar. Moser told investigators of instances where Geneva mission secretaries, including Tower's, "had been approached by the Soviets."

-Sloppy handling of heavily classified documents, including some sensitive documents that Moser allegedly kept in his car trunk. Moser also allegedly duplicated top-secret instructions from President Reagan that were not supposed to be copied. Moser, in defending himself against the accusations, alleged that in 1985 alone there were more than 375 security violations involving arms-negotiations personnel.

The government files, which were retrieved from a half-dozen federal agencies including the Pentagon and State Department, have been turned over to the Senate Armed Forces Committee, which last week abruptly postponed a vote on President Bush's nomination of Tower to the top Pentagon post, citing new information and allegations about Tower's personal life. It could not be learned if the Geneva files were related to the delay.