Senate Appropriations Committee Republicans warned Health and Human Services Secretary Otis R. Bowen yesterday that they strongly oppose his agency's proposed cuts in health and medical research outlays.

Sen. Lowell P. Weicker Jr. (R-Conn.) said he will push for at least 6,000 new and competing medical research grants for the National Institutes of Health and increased funding for a wide range of programs.

Committee Chairman Mark O. Hatfield (R-Ore.), caustically citing the argument that the federal budget deficit requires fiscal restraint in department programs, said, "We're keeping two sets of books; only nonmilitary spending creates the deficit, military spending does not."

In a separate action, Bowen named investment banker James Balog of Spring Lake, N.J., vice president of Drexel Burnham Lambert Inc., to head a public advisory group to help devise a system of nationwide catastrophic-health insurance, as directed by President Reagan.

Bowen, speaking to the National Association of Independent Insurers, said private health insurance will play a major role in this system.

In addition to the public advisory committee composed of Medicare beneficiaries, providers of health services, insurers and others, Bowen said his chief of staff, Thomas R. Burke, will head an internal executive committee working on the subject.

Technical groups are to study catastrophic illness in the under-65 population, acute-care catastrophic costs in the 65-plus Medicare population, and private financing of nursing homes and other long-term care for the elderly.

At the Senate hearing, Hatfield noted that his committee negotiated an agreement a year ago with the Office of Management and Budget by which 6,100 new and competing NIH research grants were funded in the fiscal 1986 HHS appropriation. Now, he said, Reagan wants the number cut to 5,140 over the next two years.

If these grants continue declining, Hatfield said, Reagan's Strategic Defense Initiative, which is budgeted to include 18,000 scientists and engineers, will absorb all new scientific manpower in the next few years.

The Oregonian complained to Bowen, who took over at HHS late last year, that he asked HHS 22 months ago to investigate a dispute over Medicare payments for teaching costs at Good Samaritan Hospital in Portland. Hatfield said he received a few responses but has not heard from the agency for the past nine months.