A House health subcommittee yesterday balked at the $3 billion in cuts that President Reagan has proposed for Medicare next fiscal year. Its voice vote was one of several indications that committees that supported Reagan's spending cuts last year will resist them this second time around.

The committees are balking at the specific cuts even as many of their members are deploring the budget deficits the president has projected.

Last year the congressional committees were circumvented largely as Reagan's spending proposals were wrapped together in a single bill. It is not clear whether this will happen again this year.

The health subcommittee vote came on a report to be made to the House Budget Committee, which is trying to figure out what the various legislative committees of the House are likely to do this year. The Budget Committee wants guidance for the preparation of Congress' first budget resolution for fiscal 1983 this spring.

In other recent expressions of intent affecting major benefit and other programs the president wants to cut:

* The House public assistance subcommittee declined in a unamimous vote Tuesday to commit itself to the $2.7 billion in cuts Reagan wants in Aid to Families with Dependent Children, other welfare programs, unemployment insurance, low-income energy assistance and assorted social service programs. Instead, it said the Budget Committee should count for now on all these programs going forward without cuts.

* The House Agriculture Committee, which last year cut the food-stamp program part of the way the president wanted, on Wednesday advised the Budget Committee that it did not know what cuts, if any, it would adopt among the $2.3 billion recommended by Reagan.

It said ultimate spending on food stamps could be as high as $11.7 billion, the current program carried forward without change. In a related development Sen. Robert J. Dole (R-Kan.), chairman of the Senate nutrition subcommittee, said at a recent hearing, "I do not feel we can save $2.3 billion" from the stamps program.

* Democrats on the House housing subcommittee, at a Wednesday caucus, voted to fund about 200,000 added units of low-income housing under special new rules, unanimously rejecting Reagan's proposal that no new units be funded. The full committee is expected to follow suit.

* Both the Senate Labor and Human Resources and House Education and Labor committees are expected to resist new Reagan retrenchment proposals for education and other programs under their jurisdiction.

In the Senate committee, sources said Robert T. Stafford (R-Vt.) and Lowell P. Weicker Jr.(R-Conn.) again would team up with Edward M. Kennedy (D-Mass.) and other Democrats to block cuts.

In the House committee, the president's education proposals were criticized earlier this week by Republicans, led by conservative John M. Ashbrook (R-Ohio), and Democrats, and sources in both parties predicted that most of the president's proposed cuts, which would hit college student aid programs and elementary and secondary school assistance particularly, would be rejected.

* Chairman Henry A. Waxman (D-Calif.) of the House Energy and Commerce subcommittee on health predicted yesterday that his unit would reject Reagan's proposed $2 billion in Medicaid cuts. "I don't believe the members will be willing to make further cuts in Medicaid," he said.

* The Senate Finance Committee on Tuesday promised to reduce the deficit by the same $20 billion Reagan had sought for matters under Finance's jurisdiction, but didn't say how. The general belief is that it will do so more by raising taxes, which Reagan has opposed, than by cutting benefits as he had advocated.