The House Permanent Select Committee on Intelligence has called a meeting for Thursday morning to vote on legislation that would cut off funds for covert operations against the government of Nicaragua and set up an "overt" fund of $50 million to fight gun-running to leftist insurgents in the region.

The legislation was drafted by committee Chairman Edward P. Boland (D-Mass.). But there is no certainty, according to committee sources, that the majority of Democratic members who, in secret deliberations, have supported ending the covert operations will prevail in the scheduled vote.

"It's going to be close, but we're probably going to cut it the covert operations off," one congressman said yesterday.

On the eve of President Reagan's speech to a joint session of Congress on Central America, the Senate yesterday called an unusual 90-minute secret session to hear a briefing by senior members of the Senate Select Committee on Intelligence on the covert operations in Central America. That committee also has discussed in closed deliberations new measures that would restrict current CIA activities in the region, Senate sources said.

The House legislation would amend the 1983 budget resolution to cut all funds for covert operations against Nicaragua in 45 days, giving the CIA time to "extricate" itself from support of several thousand guerrillas seeking to overthrow the leftist Sandinista regime.

After 45 days, the bill would authorize up to $50 million annually for reconnaissance, border monitoring and other arms-interdiction activities that would not involve cross-border forays into Nicaragua to strike at arms supply and other targets, which currently is the mainstay of the CIA paramilitary program.

Under the draft bill, the House Foreign Affairs Committee would be given jurisdiction over "overt" arms-interdiction funds.

Reagan met with Boland yesterday and other committee members, including Rep. Wyche Fowler Jr. (D-Ga.), who chairs the subcommittee on intelligence oversight.

After the meeting, Boland said that the committee's concerns about covert operations in the region had gone beyond questions of compliance with the Boland amendment, which prohibits U.S. assistance "for the purpose" of overthrowing the Nicaraguan government.

"I think the question now is what we do with what's going on down there and whether or not the activities we're engaged in are in the interests of the United States" and whether the operations are "really undermining the efforts of this government to establish some credibility in the area."

Fowler said of the meeting with Reagan: "We're trying to make him understand that we support his objectives in Central America . . . but the question is whether the president's policy is causing us to gain or lose ground."

Fowler said he will introduce additional legislation today giving Congress for the first time veto authority over "risky" covert operations.

Boland said Reagan defended the administration position on CIA activities in Nicaragua. "The president says the law was not broken," Boland said. "I think it's still an open question with some members who are concerned with it."

CIA Director William J. Casey, who sat in on the White House meeting, has been actively lobbying to save the CIA operation and is known to believe that the withdrawal of U.S. support for thousands of anti-Sandinista "contras" will be a devastating blow to U.S. prestige in Latin America.

Meanwhile, five House intelligence committee members returned yesterday from Central America, where they met with the presidents of El Salvador and Honduras as well as with senior officials of the Nicaraguan government.

Rep. C.W. (Bill) Young (R-Fla.) said the group had asked the CIA to arrange for a visit to a base camp for the covert operations, but was prevented from doing so by press coverage during their stay in the captial of Honduras. "We had asked to see a camp and they were prepared to take us to a clandestine, unacknowledged location," Young said, but a CIA official balked because a convoy of reporters was dogging the congressional delegation.

Young, Rep. William G. Whitehurst (R-Va.) and Bob Stump (R-Ariz.) all told reporters they believed the administration was not violating the Boland amendment when they left Washington and nothing changed their mind. "Those of us who believe in the Democratic form of government have a problem with Nicaragua and what it is doing in the area," Young said.

But Rep. Norman Y. Minetta (D-Calif.) said, "Unfortunately, I saw little to relieve my doubts about the administration's current approach to that important area of the world."