The Senate Select Committee on Intelligence agreed yesterday to fund CIA covert operations in Nicaragua for five more months, but in a 13-to-2 vote asserted a new congressional authority to veto President Reagan's covert initiatives in Central America in the future.

The compromise was worked out by committee Chairman Barry Goldwater (R-Ariz.), who told reporters in an unusual news conference after a three-hour closed session that the committee had "instructed" the president to come up with "a new program on the whole of Central America" or face a cutoff of funding for covert operations against the leftist Nicaragua government on Sept. 30.

The plan, which Goldwater said had been cleared with Reagan in a telephone call on Thursday, averted a showdown vote on a bill offered by Sen. David F. Durenberger (R-Minn.) that would have ended the covert program immediately. Goldwater's proposal drew broad support on the committee. The two negative votes were cast by Sens. John H. Chafee (R-R.I.) and Malcolm Wallop (R-Wyo.), sources said.

These sources also said that the plan reflected Goldwater's general unhappiness with the current covert program in Central America, his unwillingness to repudiate the president by cutting the program off and his belief that Congress should assert stronger authority over controversial CIA operations.

The House Permanent Select Committee on Intelligence last Tuesday reported out a bill that would bring the 18-month-old CIA program to a halt within 90 days by cutting off funding in the current budget year. The full House could vote on the measure in the next two weeks. But the Senate panel ignored the House action.

The differences between the two committees may force a House-Senate conference this summer as the deadline approaches for CIA funding in the fiscal year that begins Oct. 1.

In the meantime, it appears that CIA support for several thousand guerrillas fighting the Sandinista regime in Nicaragua will continue.

In an unusually explicit opening statement at his news conference, Goldwater said: "Actually, what we've done is fund Nicaraguan-Cuban covert paramilitary action as currently defined through Sept. 30, 1983, and authorized an additional $19 million from the reserve for contingency the CIA's secret budget to fund a new, redefined program on receipt of a new presidential finding."

A presidential finding, under the National Security Act, is a conclusion that certain foreign activities are a threat to U.S. national security and justify extraordinary covert measures to combat them.

In this case, Reagan issued a secret finding on Dec. 1, 1981, that Cuban-Nicaraguan arms supplies to leftist insurgents in El Salvador and elsewhere posed a threat to stability in the region and to U.S. interests.

Sen. Daniel Patrick Moynihan (D-N.Y.), the Senate committee's vice chairman, joined Goldwater in explaining yesterday's vote to reporters. Moynihan used stronger terms to describe what he later said was an unprecedented congressional assertion of control over covert action.

"The presidential finding will have to be approved by a majority vote of the committee," he said.

Under current law, presidents do not have to seek prior approval from Congress to initiate covert action. The National Security Act requires notification by the president, but the Goldwater compromise would advance the role of the intelligence oversight panel. Goldwater, however, appeared unwilling to acknowledge this aspect during his news conference.

"In effect, any covert action has to come before this committee for approval, if it involves funds or not," he said.

Members of the House Intelligence committee said yesterday that if the full Senate supports the Goldwater amendment the House panel likely will follow suit and assert its own authority to approve or disapprove covert action in Central America.

One House member, Wyche Fowler Jr. (D-Ga.), chairman of a key subcommittee, has proposed legislation to give both intelligence oversight committees veto authority over all covert operations.

Goldwater said the panel's action "gives the president until the end of September to continue covert action, but it also instructs him to come up with a new program on the whole of Central America, which he has agreed to do."

Asked what he expects the president to put in a new finding, Goldwater said, "I think it is perfectly plain to the president that we want a redefined position on Central America . . . . We want him to tell us in plain language just what it is he wants to do relative to Nicaragua and the other countries."

Goldwater said the compromise was not developed in conjunction with the administration. "The White House didn't have anything to present," he said. "I talked with the president on the phone . . . and I briefly outlined what we call 'alternative three,' and he found no quarrel with it."

Alternatives one and two would have continued the covert program as is, or terminated it immediately.

The Senate committee also did not duplicate House committee funding for new "overt" assistance to help El Salvador and Honduras stop the illicit flow of arms from Nicaragua to the leftist insurgents fighting the Salvadoran government. The House committee proposed to make $80 million available in the next 18 months for overt arms interdiction assistance as an alternative to funding the cross-border raids into Nicaragua currently supervised by the CIA.

Goldwater defended the House committee, which Reagan had called "irresponsible" after its vote earlier this week. "That's a bad word," Goldwater said. "I'm surprised he would use that term.