Stanford University today confirmed the controversial expulsion of student anthropologist and author Steven W. Mosher from its doctoral program and disclosed several hitherto secret charges against him.

These new allegations include attempting to break into a documents room in China and transporting top-secret U.S. papers after falsely declaring that he was a military officer with proper clearance.

The charges and Mosher's denials were released with a letter from Stanford President Donald Kennedy rejecting Mosher's last appeal of an 11-to-0 faculty decision in February 1983 to expel him.

Formally charged with "lack of candor" and other unprofessional conduct, Mosher, 37, has fought the expulsion and said he will challenge it in court.

The case of the former researcher and his activities in southern China five years ago has become one of the nation's most hotly debated issues involving academic freedom in recent years.

Since his expulsion, Mosher has published two books about his experiences in China. His report about forced abortions and infanticide there helped force a cutoff of U.S. funds to some U.N. population programs, and his supporters have charged that Stanford disciplined him to pacify Chinese officials stung by his revelations.

"Despite the fact that I was trying not to get my hopes up, I am very disappointed," said Mosher, who received Kennedy's letter today at home in Fresno.

He said Kennedy's attack on his candor was "beside the point" because he feels that he has refuted the charges against him from the Chinese government and his former wife. He noted that Kennedy now agreed that one important charge, traveling without authorization to a restricted Chinese province, appears to be false.

In his letter, Kennedy strongly denied that Chinese threats to curtail student exchanges influenced the decision. Instead, he recounted several occasions on which he said Mosher appeared to change his story about events in China, dissembled and appeared to mislead faculty advisers deliberately.

"You have destroyed the confidence of those of us at Stanford with whom you have dealt," Kennedy said.

His letter and an accompanying appendix cite many hitherto undisclosed charges against Mosher by Maggie So, his former wife. Mosher has denied them and said So threatened to get even with him when their marriage broke up.

Kennedy's letter, however, indicated that university officials accepted much of her story, particularly after Mosher declined to make more than a blanket denial of her charges before an ad hoc faculty committee probing the case.

During the year that he has reviewed the case, Kennedy said, So made additional charges, and other evidence has been collected indicating that Mosher was not candid with the university.

Kennedy quoted from a tape recording provided by So and allegedly sent to her by Mosher in 1977. In it, Kennedy said, Mosher recounts using an expired identity card from his previous naval service to take a military flight from California to Japan and says he was asked to transport secret documents.

"Don't you think it's hilarious that me, a fake naval officer and a fake holder of a top-secret clearance, got to serve as a courier and take all this top-secret material over from Travis Air Force Base to various bases in the Far East?" Kennedy quoted Mosher as saying.

Kennedy said he was not concerned by "the substance of this event" but by "the light it casts upon your mode of behavior . . . early in your graduate career at Stanford . . . ."

In the appendix, Stanford disclosed several new details from a lengthy report on So's allegations, including one that she stood watch while Mosher tried to break into a library storge room. The appendix noted that Mosher denied that the incident occurred.