After a wait of more than 18 months, the Public Health Service will soon have a permanent captain. President Reagan's nominee to be assistant secretary for health at the Department of Health and Human Services, Robert E. Windom, is expected to sail through the Senate Labor and Human Resources Committee today and to win full Senate approval in the near future.

There has been some private grumbling among department employes and on Capitol Hill that Windom, a Sarasota, Fla., internist, has more political experience and less public health experience than most of his predecessors.

Windom has been a stalwart in Republican Party politics. Windom's curriculum vitae lists him as the 1980 chairman of the Florida Physicians for Reagan Committee, chairman of the Reagan-Bush '84 Reelection Regional Committee for Florida, Georgia and Alabama, and an alternate delegate to the Republican National Convention in l984.

McGraw-Hill's Washington Report on Medicine & Health reported that, according to Federal Election Commission records, Windom gave about $55,000 to Republican political campaigns between 1979 and 1984, mostly to GOP Senators, including committee Chairman Orrin G. Hatch (R-Utah).

But Windom has the support of Hatch, who "has no reservations at all," an aide said. And Sen. Edward M. Kennedy (D-Mass.), the ranking minority committee member, is expected to vote for the nomination, despite his complaints that Windom's qualifications do not match those of many of his predecessors, who generally have been biomedical research scientists, directed major academic medical centers or institutes or had previous federal health positions.

The assistant secretary's responsibilities include the National Institutes of Health, the Alcohol, Drug Abuse and Mental Health Administration, the Centers for Disease Control, and the Food and Drug Administration.