After almost two decades on the sidelines, Congress -- for better or worse -- is back in the business of setting federal and military pay raises.

Senate-House conferees meeting on a revised budget yesterday set a 6.2 percent limit on this October's white collar federal pay raises. They put an 11.7 percent cap on military compensation.

The action in support of resolutions from the powerful Senate and House Budget Committees is a temporary blow to President Carter's plan to win federal pay reform this year. But the 6.2 percent ceiling is the same that Carter's pay reform plan would have produced if Congress had okayed it. If all this sounds complicated it is because Congress is plowing new ground, quickly, and this makes for a complicated situation.

Since the mid-1960s, federal-military pay has been set by the president under a complex, catchup-with-industry system called pay comparability. In effect, Congress was reduced to having a veto over pay raises proposed by the president.

Insiders say the budget committee conferees yesterday were on the road to approving language that would have mandated the House Post Office-Civil Service Committee, and the Senate's Governmental Affairs Committee, to approve Carter's controversial pay reform bill this year as part of their share of savings ordered by the budget committees.

Federal union leaders generally oppose reform because of the extra powers it gives the president to set raises using new comparison techniques, and the fact that reform would have produced a 6.2 percent federal pay raise rather than the 11 percent-plus due -- but not guaranteed -- under the current comparability law.

In effect the budget committee conferees have endorsed the figure -- 6.2 percent -- in Carter's pay reform but have not ordered the two jurisdictional committees to approve reform itself.

Rep. Gladys N. Spellman (D-Md.) is credited with lobbying the budget committee successfully. She -- and many other members of Congress -- have objected to letting the Budget Committees order jurisdictional committees to report out specific legislation.

Carter administration aides warn that the antireform action could backfire. With reform, they argue, the president could (and would) have ordered a 6.2 percent raise. And sold it to the public as being justified, based on a fair comparison of government vs. industry wages and fringe benefits. Without reform, however, they say the 6.2 percent figure is merely a budgetary target that conservatives -- and here read GOP front-runner Ronald Reagan -- could attack, and perhaps cut back.

Carter aides disagree with the assessment that the conferees' action is a "blow" to pay reform. "In fact," one said, "the Congress has agreed to accept the rationale that produced a 6.2 percent recommendation from Carter. That recommendation was based on the structure of pay reform. If they (the Congress) don't accept pay reform by statute, it opens the process up to politics every year, determining federal pay raises based on the political climate of the day, not a data showing the relationship of federal pay vs. industry pay."

Unions and their congressional allies say the Carter approach is "blackmail." The choice, they say, is take reform and 6.2 percent or kill reform, and perhaps get less. Like nothing.

This isn't the end of the episode. Appropriations committees will have to formally approve the 6.2 percent federal pay cap. The Carter people will keep pushing for federal pay reform this session.

For now, Congress is back in the pay-fixing business. In the curious position of having endorsed Carter's pay conclusions without having okayed the method he used to arrive at them.