Rejecting Pentagon pleadings, two key congressional subcommittees yesterday moved to raise the pay of specialists in the armed services more than that of privates and seamen.

In doing this, the House defense appropriations subcommittee and the Senate Armed Services manpower subcommittee junked President Reagan's proposal to give everybody in the military a 5.3 percent raise this July and another 9.1 percent increase on Oct. 1, the start of fiscal 1982.

Although the Pentagon had given up on getting the 5.3 percent increase in July, it had hopes of persuading Congress to lump that raise in with the 9.1 percent increase.

The House Armed Services Committee has gone along with this approach by approving a bill calling for a 14.3 percent increase for all 2 million men and women on active duty, effective Oct. 1.

Because such a big raise would bust the congressionally set budget ceilings, the House defense appropriations subcommittee met yesterday to shave it down.

The subcommittee agreed to cut the fiscal 1982 raised from 14.3 percent to 9.1 percent, with the understanding that Chairman Joseph P. Addabbo (D-N.Y.) will move to go beyond that. He intends to recommend that the House adopt a plan approved yesterday by the Senate Armed Services manpower subcommittee once the bill reaches the House floor this month.

This is to recommend that critical specialists and rates get bigger raises rather than everybody's pay being increased by the same percentage.

Under the Senate subcommittee bill, sponsored by Sens. Roger W. Jepsen (R-Iowa) and J. James Exon (D-Neb.), the beginning private, seaman or airman would receive a pay raise of 7 percent. But the veteran sergeant, aircraft mechanic or Navy petty officer would get raises of up to 22 percent, starting Oct. 1.

The argument is that these are the specialists the all-volunteer military must keep to be ready to go to war. Similarly, the biggest raises for the officer corps would go to the middle-management ranks rather than beginning lieutenant or the generals.

Backers of the Jepsen-Exon approach say such graduated pay raises would total between $4 billion and $4.4 billion, compared with $5 billion for the Reagan proposal for fiscal 1982.

Shortly after the House defense appropriations subcommittee acted yesterday, the Pentagon held a news conference where Lawrence J. Korb, assistant secretary of defense for manpower, said the administration opposed targeted raises.