Dr. John F. Finklea has resigned as director of the National Institute for Occupational Safety and Health after nearly three years as head of the controversial occupational health research agency.

Finklea's abrupt departure from NIOSH friday was not publicly announced. Finklea did not offer any specific reason for leaving in a letter of resignation he sent to Dr. William Foege, head of the Center for Disease Control, which has jurisdiction over NIOSH.

Federal officials and others familiar with NIOSH said yesterday, however, that Finklea was under pressure to resign after more than a year of bureaucractic feuding with officials within his own agency as well as with others in separate regulatory agencies and in Congress.

Finklea, 43, is a former medical school professor who headed the Environmental Protection Agency's National Environmental Research Center before he was appointed head of NIOSH in March, 1975. He could not be reached for comment yesterday.

The decision to appoint finklea was seen by some observers as a hardening of the federal government's stance against companies that pollute the workplace. Since he took over the job NIOSH has identified 65 potentially dangerous substances found at job sites, a sharp increase over the 23 such warnings issued during the first four years of NIOSH's existence.

But Finklea was accused by critics both inside and outside the federal research agency of being 3 difficult administrator who lost a number of its key research personnel during his tenure.

Although the entire federal worker health program is under review by President Carter's reorganization task force, knowledgeable federal officials said yesterday Finklea's resignation did not indicate any immediate change in the agency's current status as an arm of the Department of Health, Education and Welfare.