Rafael L. Cortada, the president of the University of the District of Columbia, has removed three top academic officials he appointed when he took office three months ago.

Two of the three, William Couch, the acting provost and vice president for academic affairs, and Wilmer L. Johnson, acting associate provost, had been embroiled in a bitter controversy with leaders of the Faculty Senate, which Johnson used to head.

The shake-up was "totally unrelated" to the dispute, said Cortada, who has had to contend in his brief tenure with warring campus factions and the appearance of an underground newsletter attacking several top UDC officials.

Cortada said he has appointed Albert Jose Jones, acting dean of life sciences, to the acting provost's job because of his scientific background and technical expertise. He said Jones will direct the detailed planning of the major reorganization of the university that Cortada plans to submit to the UDC Board of Trustees this month.

"Dr. Couch has gotten the administration off to an excellent start," Cortada said. "I'm very grateful. Now we're moving into a more technical phase."

Cortada said the departure of Johnson and Mohamed A. El-Khawas, the other acting associate provost, was "the normal consequence" of a change in provost.

Both men will return Monday to their regular faculty positions. Johnson is a professor of health, physical education and leisure studies. El-Khawas is a professor of history.

Last month the Faculty Senate urged Cortada to remove Johnson as acting associate provost. Couch strongly supported Johnson and in a memo urged the president to issue a public statement rejecting allegations made against him by some faculty members. Cortada said he decided not to do so because D.C. Auditor Otis H. Troupe had begun an investigation.

Troupe is probing allegations that Johnson was paid improperly last summer when he taught no courses but did administrative work, and that he changed an evaluation form to get a pay raise.

Acting at the request of several faculty members, the university's internal auditor, Samuel A. Halsey Jr., issued a report in late November recommending that the university "seek restitution for the evident overpayment" for Johnson's summer work.

Halsey said he was unable to determine who changed Johnson's evaluation form but recommended that the evaluation be repeated and the pay raise suspended.

Johnson strongly denied any wrongdoing. Couch said there was no evidence that Johnson had done anything wrong and said the payments he received were in line with university policy.

Last winter Johnson, who had been president of the Faculty Senate for l0 years, supported a study group that recommended faculty layoffs because of falling enrollment. The number of students at UDC has declined by about one-third in the past eight years.

In April, Johnson was ousted as president of the Faculty Senate and succeeded by Emanuel D. Chatman, vice president of the the faculty union, which strongly opposed any faculty cuts.

The trustees laid off 44 faculty members last summer, about an 8 percent reduction.

Yesterday Couch, an English professor who retired several years ago, said, "I agreed to help out {Cortada} until the president got on his feet . . . . Now I'd just as soon get back to a calmer climate."

Jones, the new acting provost, is a professor of environmental science. He taught at Washington Technical Institute until it merged to form UDC in 1977. Born in the District, he holds a doctorate from Georgetown University. He also is an expert scuba diver and skier, holds a black belt in karate and drives to campus in a red Corvette.

Cortada said he has not yet named an associate provost.