The Reagan administration, in an attempt to break an impasse with Congress over medical research, has agreed to make 5,500 new National Institutes of Health research grants for each of the next three years instead of the 5,000 proposed in the president's budget for fiscal 1986.

The agreement was embodied in the deficit-reduction package worked out by the administration and Senate GOP leaders April 4. However, it does not address a dispute over the number of grants that will be funded this year. Congress last year provided funds for 6,500 new grants, but the administration has said it will fund only 5,000.

Some key members of Congress also are not happy with the current compromise for the next three years, saying that it would not support enough grants.

Sen. Lowell P. Weicker Jr. (R-Conn.), chairman of the Appropriations subcommittee with jurisdiction over NIH, still wants to provide 6,500 new grants -- this year and for the next three. Aides to Rep. Henry A. Waxman (D-Calif.) and Sen. Edward M. Kennedy (D-Mass.) said they also aren't satisfied with the new proposal.

Edwin L. Dale Jr., spokesman for the Office of Management and Budget, said, "We have made a compromnise, definitely, from our original proposal of 5,000."

Weicker said through an aide, however, that he doesn't think 5,500 is enough, and that he doesn't like the April 4 compromise because it cuts some crucial programs for the poor and ill. "The compromise dumps on those who suffer physically, mentally and economically. I oppose it," he said in a statement.