Days before the Nuclear Regulatory Commission reinstated its chief inspector last week, the Justice Department warned the commission that it had found evidence of serious improprieties in the way she handled a discrimination complaint filed by a subordinate.

A senior Justice Department official said in a letter that there is "clear and convincing evidence" of improper conduct by Sharon R. Connelly, director of the NRC's Office of Inspector and Audit and that "meaningful administrative action" should be taken against her. But the commission took Connelly off administrative leave and returned her to her job.

"We have decided to defer institution of criminal charges until we can assess whether administrative action to be taken against Ms. Connelly satisfies the interests of justice," Lawrence Lippe, chief of litigation for the Justice Department's Criminal Division, told the NRC in the March 22 letter.

Lippe said the department had offered to drop the case if Connelly could pass an FBI polygraph test, but that she declined to take one, while her chief accuser agreed to such a test.

Connelly's attorney, August Bequai, called the letter "outrageous" and "irresponsible" and said it turned "allegations made by one individual . . . into a de facto finding of guilt."

"There really isn't a case here," Bequai said yesterday. He added that Connelly had a legal right to decline a polygraph test and that he had advised her not to take it.

An NRC spokesman said yesterday the commissioners stand by their statement that they found the allegations unsubstantiated and retain full confidence in Connelly. A Justice Department official declined to comment on whether further action would be taken in light of the NRC's handling of the matter.

Connelly was placed on leave Jan. 28 after Rep. Edward J. Markey (D-Mass.) asked the NRC to look into allegations of "serious impropriety" in the the way she and two deputies handled a sexual harassment complaint. The complaint was against Connelly's deputy director, George Messenger, who has since been detailed to another job.

Messenger's attorney, Richard Jordan, said yesterday that Messenger did nothing improper and has passed a polygraph test to support his account.

On Sept. 11, 1985, according to Lippe's letter, Connelly reviewed the personnel and security files of Lisa Shea, a former auditor in her office who had filed an equal employment opportunity (EEO) complaint against Connelly and Messenger the day before.

Under the Privacy Act, Lippe said, "records may not be pulled for an improper purpose," such as "a privately conducted fishing expedition to obtain 'dirt' against an employe to discredit them in an EEO proceeding."

Connelly said she did not know of Shea's complaint and reviewed her files to check a possible inconsistency in her academic credentials, according to Lippe's letter. He said this explanation "does not make sense in view of the facts."

"We believe there is, at least, clear and convincing evidence that Ms. Connelly knew prior to the time she requested Lisa Shea's personnel and security files that Ms. Shea was about to file or had filed an EEO complaint, and that such a filing would be contrary to Ms. Connelly's . . . best interest," Lippe said.

On two occasions last year, he said, "Ms. Connelly made troublesome, if not intimidating remarks to Ms. Shea to discourage her from filing an EEO complaint."

Attorney Bequai said it is "ridiculous" to suggest that Connelly urged Shea not to file a complaint. He said Connelly was entitled to review the records and that "there is no evidence. . . that Ms. Connelly violated the law."

Lippe charges that Connelly and her attorney have tried to divert attention from the case by making "derogatory references" to Shea's personal life. Bequai called this allegation "pure nonsense."