Thomas A. Wilkins has been removed as head of the District of Columbia's troubled Department of Labor and will be replaced on an interim basis Tuesday by mayoral aide Mathew Shannon, a Barry administration official said last night.

Wilkins, 50, has been head of the city's manpower operations since 1972 and acting director of the Department of Labor since it was created by a governmental reorganization last June. He is the fifth agency head to be removed since Marion Barry became mayor Jan. 2.

The reshuffling of the agency left in doubt the tenure of Lorenzo M. White, who, as acting deputy director, is regarded as the department's key administrator.

The department has been criticized frequently for bureaucratic snarls and infighting and has been accused of cronyism and ineffective delivery of services.

Shannon, 29, who will become acting director, is an attorney who is special assistant to the mayor for labor relations and religious affairs. He filed for the Democratic nomination for the Ward 5 seat on the City Council last year but withdrew from the primary campaign after he was injured in an automobile accident. He now is recovered.

The administration official who confirmed the departmental shift said Shannon definitely is an interim appointee and is not being considered for permanent assignment. The official asked not to be identified.

Wilkins, a veteran of 21 years of government service, became head of the city's manpower office when it was part of the U.S. Department of Labor. He became a city employe when the department was brought under city jurisdiction as home rule took effect in 1975.

Unted existing law, however, he retains U.S. civil service job rights, including his GS-16 grade and $47,500 annual salary. The Barry administration official said Wilkins will be returned to federal service under terms of the federal Interagency Personnel Act.

The official said the Wilkins and Shannon reassignment were to have been announced after they had taken place.

Wilkins had been on the so-called "hit list" of officials Barry had targeted for removal. He was especially vulnerable, since former mayor Walter E. Washington designated him as acting director, rather than director, when the Department of Labor was created.

Wilkins is the fifth top-ranking agency administrator to be removed by Barry. Those previously ousted included the heads of the housing, licensing, human rights and municipal planning agencies. At least eight other key subordinates have been demoted or reassigned.