As time was running out for meeting payrolls for thousands of federal employes, House and Senate conferees failed yesterday to reach agreement on two issues -- a congressional pay raise and federal funding of abortion -- holding up a vital funding resolution.

Conferees thought they had agreement on the abortion issue.

House members who had consistently insisted that federal funding of abortions should be limited to cases where the life of the woman is in danger agreed to a proposal by Senate conferees. That proposal was to include cases of rape and incest if promptly reported.

However, that agreement fell apart when the Senate refused to accept a 5.5 percent cost-of-living increase for Congress that the House wants.

The conferees will meet again today.

Meanwhile, time was running out for major government departments that have had no funding since Oct. 1, the start of the new fiscal year, because Congress has not passed their appropriations. House Appropriations Committee Chairman Jamie Whitten (D-Miss.) suggested late yesterday that Congress might pass an emergency resolution giving the government departments enough money to meet payrolls and pay benefit checks for a week or so while the conferees continue to argue over the pay increase and abortion issues. But it was not clear whether his suggestion would be accepted.

If something like that suggestion is not approved, or the dispute is not resolved by the weekend, 1.6 military personnel will not get paid next week, and thousands of federal employes -- including 22,000 at the Labor Department, 68,000 at Transportation and 600,000 at Defense -- face half pay if it is not resolved today.

Most of the sessions between the House and Senate conferees yesterday were taken up by a shouting match over the congressional pay increase issue.

The resolution includes a 5.5 percent cost-of-living increase for high-paid officials in the executive branch and federal judges. Congress was included in the increase, but while the House has voted for it, the Senate has turned it down.

Yesterday, House conferees accused senators of being uninterested in the 5.5 percent pay increase because the senators gave themselves a back-door raise by lifting a limit on outside income.

The limit of $8,625 was included in a new congressional ethics code in 1977. That year Congress also voted itself a $12,900 pay increase on the recommendation of a commission which also suggested Congress should limit outside income in return.

However, in 1978 the Senate suspended the limit until 1983. Now senators can make up to $25,000 a year in honoraraia for speeches and an unlimited amount from business ventures and other sources.

An angry Senate killed the funding resolution after the House voted for both the 5.5 percent pay raise and tough abortion language, and then adjourned for 10 days, leaving the Senate in a take-it-or-leave-it position.

During the debate, Sen. Edmund S. Muskie (D-Maine) called House members "devious fools," and Sen. Barry Goldwater (R-Ariz.) called them "scoundrels."

In a response yesterday, Rep. Silvio Conte (R-Mass.) said that since the Senate had "reneged" on the outside-income limit, Muskie has made $25,000 and Goldwater $24,000 in honoraria.

"Those are the guys who ought to be shamed. Shame on you, Barry Goldwater," Conte shouted. "You know who invited them to speak. Look at the legislation and who invited them to speak, it was those special interests who had legislation before their committees."

Rep. Robert H. Michel (R-Ill.) joined in: "One-third of the Senate are millionaries. One-seventh of the House are millionaires. Sure, why should you in the 50 percent tax bracket bloody your nose over this little raise. Sure it's not worth it."

Senators had offered to let the House take the raise, while turning it down for themselves. House members said they would do that only if the Senate restored the income limit.

"Senate rules are not before this conference," Sen. Ted Stevens (R-Alaska) said. Then he offered to do that if the House would accept the Senate's more lenient language on abortion. House members angrily retorted that the two issues should not be tied together.

Some progress was made on abortion, however. The House traditionally votes for language that would allow federal funding of abortions only where the life of the woman is endangered.

Current law allows federal funding for abortions where the life of the woman is endangered, in cases of rape or incest, or where two physicians certify that continued pregnancy could result in lasting damage to the health of the woman.

Sen. Warren Magnuson (D-Wash.) offered to drop the condition of severe or lasting health damage. However, Stevens said that would not be acceptable to the Senate and wanted to substitute language allowing funding for abortions where the future child-bearing capability of the woman was endangered.