Defense Secretary Frank C. Carlucci testified yesterday that he believes President Reagan would probably veto any legislation requiring that all covert operations be reported to Congress by the administration within 48 hours.

Legislation making congressional notification mandatory is the chief proposed policy change to grow out of the Iran-contra affair, which was conducted as a covert operation, and the Reagan administration has declared all-out opposition. Carlucci requested to appear before the Senate Select Committee on Intelligence yesterday to voice his disagreement with the legislation drafted by its vice chairman, Sen. William S. Cohen (R-Maine).

Carlucci said he had instituted major reforms and new procedures at the White House for covert operations during the last year, when he served as national security adviser before moving to the Pentagon. These reforms, he said, would prevent a repeat of the Iran arms sales operation that was kept secret from Congress for 10 months.

"I believe the problems in the executive branch are behind us and that we have learned from recent events," he said, noting that the president had a new CIA director, William H. Webster, and a new national security adviser, Lt. Gen. Colin L. Powell. "Why not give the new system and new team a chance to work?"

On the matter of mandatory notification, Carlucci said, "The president feels very strongly on this issue, so strongly in fact that should it reach his desk in this form he may well see fit to disapprove the bill."

However, former CIA deputy director John N. McMahon disagreed with Carlucci, telling the committee, "I would endorse the 48-hour rule."

McMahon said Congress should not leave the reporting requirement open-ended. Echoing a theme he frequently repeated in his four years as deputy to the late CIA Director William J. Casey, McMahon said Congress should protect the agency. When a covert operation fails, he said, "the organization that pays the price is the Central Intelligence Agency, not the presidency."

The president, in an Aug. 7 letter, said he would notify the intelligence committees of covert activities within 48 hours "in all but the most exceptional circumstances." It is this exception that Cohen's legislation would eliminate. "This would not take away one yard or one foot of the president's power," Cohen said. "All the committees want is to be informed."

Covert actions include any attempt to interfere in the affairs of foreign countries, such as clandestine propaganda or assistance to a foreign political party, and military aid, such as that to rebels fighting Soviet-backed governments in Nicaragua and Afghanistan.

Carlucci yesterday released a six-page declassified extract from a presidential National Security Decision Directive that outlines the new procedures for notifying Congress of covert operations. It provides in part that in "rare, extraordinary circumstances," which are not further defined, the president can delay notification as long as he chooses.

This loophole requires only that the reasons for delaying notification be put in writing and that the decision not to notify Congress be reevaluated at least every 10 days by the Cabinet members who make up the National Security Planning Group.

Of particular concern to Congress, Cohen said, are U.S. covert operations with foreign governments and intelligence services, which often expect some overt or covert favor in return for cooperation. "Someone in Congress should know," Cohen said, because of a likely exchange of favors between U.S. and foreign intelligence agencies.

Carlucci said that if foreign intelligence services, which provide critical information in fighting terrorism and narcotics traffic, perceive that the CIA has no control over what information is provided to Congress, they will cease to cooperate.

"If there are no boundaries," he said, "intelligence assets will dry up." He said he knew of "numerous" occasions when foreign governments had said they would not share information if the CIA provided it to Congress.

Carlucci, President Jimmy Carter's deputy CIA director, said Carter believed it important to preserve the option of nondisclosure to Congress in operations that risked lives.

Cohen, noting that lives are at stake in most covert operations, questioned how the administration could determine which operations might be withheld. Regular covert operations such as the CIA's paramilitary assistance to the Nicaraguan and Afghan resistance are routinely reported to the intelligence committees.

Carlucci said "this is a fundamental separation of powers issue" about the authority of the president to act in foreign affairs, especially during a crisis, and he urged that at a minimum the committee delay action on the Cohen bill.

Undersecretary of State Michael H. Armacost also testified against the legislation, saying it would be "an infringement on the president's constitutional power."