In less than four minutes and with fewer than a dozen members on the floor yesterday, the House once again whipped through a 5.5 percent pay increase for members of Congress.

The action sets up another confrontation with the senate in what has become a grudge match between the two bodies over the issues of abortion and congressional pay.

The floor action came so fast yesterday that House opponents of a congressional pay raise were caught unaware. Rep. Charles E. Grassley (R-Iowa), who said he wanted to offer an amendment to knock out the raise, said he was off writing his amendment when the voice vote came and went. Another Democratic member, who said he was opposed to the raise, was in a telephone booth while the action went on.

The Congressional raise was attached to a vital funding resolution to continue operations for most of the government. Government departments involved have been operating on leftover money since Oct. 1, the start of the new fiscal year. The continuing resolution is to fund those departments until congress passes their regular appropriations bills.

How long the government can function is a matter of debate. House Speaker Thomas P. (Tip) O'Neill Jr. (D-Mass. said yesterday there will be no emergency until the end of the week, but some senators have contended that some payrolls and programs will be affected before then.

In its action yesterday the House also rolled back to 5.5 percent a 12.9 percent pay increase federal judges and executive branch officials making more than $47,500 automatically became entitled to Oct. 1.

Since the constitution says the pay of federal judges may not be lowered while they are in office, Rep, Silvio A. Conte (R-Mass.) admitted that the language rolling back the raise for the judges "isn't worth the paper it's written on" but that it would force the judges to go to court to get their money.

Then, the House passed a separate resolution to fund the departments of Labor and Health, Education and Welfare until Sept. 30, 1980. To this resolution they attached the controversial amendment insisting on strict antiabortion language, denying federal funding of abortions except where the life of the woman is endangered.

The vote for the strict abortion language was 234 to 162.

It is the entanglement over abortion that has caused the fight between the House and the Senate. Two weeks ago, after an agonizing three attempts, the House passed a resolution giving Congress, along with the executive and judicial branch members, the 5.5 percent pay raise.

But the Senate refused to give the raise to Congress, intending instead to use the raise to force the House to back off from its tough anti-abortion language and accept the milder Senate language instead. Senate language, which is current law, permits abortions for rape, incest and where severe health damage to the mother would result.

In a House-Senate conference, the Senate thought it had a deal: the House would take the raise and back off on abortion. Instead, House members rushed back to the House floor, voted for both the raise and the House position on abortion, then adjourned for a 10-day recess.

The action left the Senate holding the bag and fuming. Sen. Edmund S. Muskie (D-Maine) called the House members "devious fools," and the Senate voted to kill the resolution.

Last week, while the House was in recess, the Senate again passed the resolution, knocking out the congressional pay increase and insisting on the Senate language on abortion.

A leadership aide said the House's strategy is to try to force the Senate to face the pay raise issue apart from the abortion issue.