The House Foreign Affairs Committee spent more than five hours behind closed doors yesterday questioning CIA and State Department officials on the efficacy of large-scale covert operations in Nicaragua.

But the committee did not vote on a measure that would end the "secret war" within 90 days.

The legislation, approved by the Democratic majority of the House Intelligence Committee last week, would replace covert support for guerrillas fighting the leftist government of Nicaragua with "overt" assistance to neighboring countries to stop arms traffic to leftist guerrillas in El Salvador. The overt assistance, $80 million over the next 18 months, would have to be authorized by the Foreign Affairs panel.

The bill was sponsored by Reps. Edward P. Boland (D-Mass.), Intelligence Committee chairman, and Clement J. Zablocki (D-Wis.), Foreign Affairs chairman. Several members of the Foreign Affairs Committee said the vote had been postponed until Tuesday.

Also, House Majority Leader James C. Wright Jr. (D-Tex.), an ex-officio member of the intelligence panel, said a planned secret session of the full House before it votes on the bill would not be held until after the Memorial Day recess.

Wright told reporters that many members of the committee are seeking "some commonality" to prevent the issue from becoming "a bone of partisan contention."

He would not say whether there is any move toward accommodation with the Republican-controlled Senate Intelligence Committee, which voted last Friday to continue the covert aid only until Sept. 30 unless President Reagan comes up with a new justification for the CIA operation.

The House Foreign Affairs panel conducted a question-and-answer session with administration witnesses, including Deputy Secretary of State Kenneth W. Dam, Deputy CIA Director John McMahon and Powell A. Moore, assistant secretary of state for congressional relations.

In what several members described as forceful testimony, Wright conveyed his view that the leftist Sandinista regime in Nicaragua had betrayed the promises of its revolution, but that U.S. support for covert operations against it is hurting American credibility in the region and the world. At the same time, he strongly urged continued support for the government of El Salvador in its fight against Nicaraguan-aided insurgents.

"I think the Boland-Zablocki bill, by providing money for arms interdiction of supplies through help extended to other countries in the region, but not in a covert way,...would make it clear that people want to stop the flow of arms to Salvador," said committee member Stephen J. Solarz (D-N.Y.), "but not in the manner pursued by President Reagan, which doesn't appear to be very effective."

Rep. Robert G. Torricelli (D-N.J.) said administration witnesses emphasized the bill's impact on the estimated 7,000-man U.S.-backed guerrilla force now operating in Nicaragua.

"The moderate element of the committee appears willing to compromise," he said. "I'm disappointed, ...because American laws are being violated and a sovereign nation is being invaded and those are two actions that defy compromise."

Meanwhile, the Senate Foreign Relations Committee voted unanimously yesterday to require more frequent and detailed reports by the Reagan administration on El Salvador's progress toward halting "terrorist activities by so-called political extremist 'death squads' " operating in that country. The amendment, calling for reports every six months, was offered by Sen. John Glenn (D-Ohio).