When the Reagan administration set out to cut the budget of the National Health Service Corps, it may have gotten more than it bargained for.

Unless the corps gets some of its cuts restored, 200 doctors that the government has put through medical school may have to be freed of their obligation to work for the government in areas that are short of doctors.

That warning comes from Health and Human Services Secretary Richard S. Schweiker, who says the program needs $9 million more if it is going to be able to pay the salaries of the newly trained doctors.

Since 1974, the government has been paying room, board, tuition, fees and a monthly stipend for living expenses to some medical students and a handful of other health professions trainees who might otherwise not be able to attend medical school.

The cost per student is substantial: tuition to medical school can cost more than $10,000 a year and the government pays each student about $512 a month for living expenses. In fiscal 1981, about $63 million was spent on such scholarships.

There was only a handful of new scholarship recipients for the current academic year because of Reagan administration budget cuts and the view that doctor shortages are ending.

But about 4,200 students who started school in earlier years had their scholarships renewed and are still being trained at government expense, program officials said yesterday.

Under the program, the student doesn't have to pay anything back: he only has to enroll in the corps and serve one year in an area that has a shortage of health professionals for each year of support the government provided (with a minimum of two years). For that, students get a salary that can run as high as $38,000 a year for those who have finished their residency, according to program spokesmen, but do not have to repay the government for their education.

The corps serves in places like Indian reservations, inner-city storefront health clinics, federally funded primary health care centers for the poor, and isolated rural areas. The government now has several thousand in the field in these kinds of jobs.

The agency's request for funds to put professionals in the field after they've finished their training has been altered several times. According to the House Appropriations Committee, the administration request was recently chopped several million dollars to $90.8 million.

It is possible the problem can be avoided, Schweiker and others said yesterday. For one thing, Congress may well provide more money than requested, and the House has already moved to do so.

Moreover, a committee aide said, the program has a "private practice option." If the student prefers not to work in a reservation or federally funded clinic, he or she can satisfy the requirement by working in one of the areas, but in a facility run by someone else, such as a state or county clinic. About 412 people on federal scholarships went to work for such facilities in fiscal 1981; the hope is to channel more people into those facilities if the federal government doesn't have the money to employ them.

And Schweiker said in an interview he is exploring a variety of options to try to make sure the government doesn't lose the services of these highly trained young medical personnel.