A panel of nuclear experts agreed yesterday that the Iraqi nuclear reactor that was destroyed last week by Israeli warplanes could well have been part of a clandestine nuclear weapons program, but they disagreed over whether such a program would have escaped detection by international agencies.

Testifying before the Senate Foreign Relations Committee, Roger Richter, an American who resigned last week as an inspector for the International Atomic Energy Agency, said he has no doubt that Iraq intended to use the reactor to produce plutonium for use in nuclear weapons and that the IAEA would not have known about it.

Because of a variety of "loopholes" in its powers and procedures, Richter told the committee, "the IAEA is incapable of safeguarding a facility of this type."

But another member of the panel, Dr. Herbert J.C. Kouts, chairman of the department of nuclear energy at Brookhaven National Laboratory in in New York, said it would be difficult for the Iraqis to run a secret weapons program without detection, if not by IAEA inspectors then by the French technicians who helped build the reactor and were to remain until 1989 to help run it.

Ritcher, Kouts and Dr. Robert Seldon of the Los Alamos Laboratory in New Mexico testified on the second day of Senate hearings on the June 7 Israeli raid on the French-built reactor outside Baghdad.

The Senate committee and the Reagan administration are reviewing whether the use of American-supplied F16 fighter-bombers in the attack violated Israel's agreements with the United States on the use of American weapons. Yesterday's testimony centered on technical aspects surrounding Israel's main defense of the raid -- that it was a justifiable act of national self-defense because Iraq intended to use the reactor to produce nuclear bombs for use against Israel.

The three scientists agreed, in Seldon's words, that the reactor could produce enough plutonium for a "small weapons program," but probably not for at least a few years. Seldon and Kouts also expressed less certainty than Richter that this was the Iraqi intention and that it could have been accomplished without detection.

Kouts' contention that a weapons program probably would have been detected was buttressed by a report on the raid controversy made public yesterday by the foreign affairs and national defense division of the Congressional Research Service.

The report concluded that a crash program to produce plutonium in the reactor would quickly be detected by the IAEA. If Iraq chose to conceal its intention by producing only a small amount of plutonium, the report said, "it would not soon have enough to do the necessary experimental work, to learn how to handle this material and fabricate it, and to have enough left over for a nuclear weapon."

Richter's appearance before the Foreign Relations Committee was arranged by Sen. Alan Cranston (D-Calif.), the panel's most outspoken defender of the Israeli raid. In his testimony, Richter portrayed the IAEA as having severely limited powers and procedures for the tasks it is charged with accomplishing.

For example, he said, because certain key facilities at the Iraqi nuclear installation are not subject to IAEA safeguards, and because advance notice must be given of IAEA inspections, Iraq could produce plutonium in the reactor and move the material out of it before inspectors arrived.

By such techniques, Richter said, Iraq in a few years could produce enough plutonium for several atomic bombs, all the while mastering the techniques needed to fashion the plutonium into a nuclear device.