A House-Senate conference committee agreed yesterday on a scaled-down $5.5 billion emergency spending bill aimed at avoiding a third veto by President Reagan, who wanted less than $5 billion in new spending authority.

There was no immediate comment from Reagan, who vetoed two larger versions of the measure as too costly. But Senate Appropriations Committee Chairman Mark O. Hatfield (R-Ore.) said he thought Reagan would sign the bill if, as expected, it is approved by the House and Senate. Final congressional action is expected today or tomorrow.

Even if Reagan signs the bill, however, there could be more appropriations squabbles because House members plan to add some of the items cut from the so-called "urgent" supplemental appropriations bill onto another supplemental money bill for the rest of fiscal 1982. The House Appropriations Committee is scheduled to mark up that bill today.

The second supplemental is expected to be roughly double the size of the first and will include money for military pay raises.

The two bills previously vetoed by Reagan were a $8.9 billion version that included $3 billion for mortgage subsidies to prop up the housing industry, and a $5.9 billion version with the housing money taken out. Democrats made attempts to override the vetoes in the House, but the vetoes were sustained.

Before leaving for its July 4 recess, the Senate approved a $5.3 billion alternative that was worked out in advance with Office of Management and Budget Director David A. Stockman, and most of the debate in conference yesterday was over spending add-ons sought by the House.

Among the add-ons accepted by the conferees was $45 million for summer youth jobs, $20 million for refugee assistance, $72 million for highways and $42 million for postal subsidies. The additional spending was offset in part by a $22 million cut from money approved by the Senate for the work incentive program and $171 million more in longterm rescissions of spending authority for rent subsidies for the poor.

House members wanted more add-ons, but Hatfield argued repeatedly that Reagan would probably veto any spending that exceeded the Senate's proposal. "I want to get this matter behind us," he said wearily of the marathon battle over the measure.

House Appropriations Committee Chairman Jamie L. Whitten (D-Miss.) protested that the Senate's compromise with Stockman deprived the House of its prerogatives and amounted to an "item-veto" of appropriations by the White House. Rep. Silvio Conte (R-Mass.) joined in the protest, complaining that Stockman and the Senate had made "God-darned orphans out of us."

Denying Whitten's charges that Congress was abdicating its appropriations responsibilities to the White House, Hatfield said Stockman did not dictate specific program cuts and added: "The president has also been elected by the people, and he has a role in this process too."

The bill provides money for a dozen or more agencies that are facing employe furloughs because their money has run out, along with $1.3 billion for guaranteed student loans, $2.4 billion for sewer grants and $1 billion for food stamps. It also includes $5.9 billion in housing program rescissions and repeal of a $75-a-day tax deduction for Washington living expenses of members of Congress.