In the shadow of the continuing "cold peace" between Egypt and Israel, 50 Israeli and Egyptian scientists are meeting here for the first time to discuss the results of six years of quiet cooperation.

This rare open manifestation of Arab-Israeli cooperation has produced, among other things, a new species of goat, a hybrid fish and a new kind of desert shrub.

The three-day conference, which opened here yesterday, grew out of the U.S.-financed Middle East Regional Cooperation program that has brought together more than 1,000 scientists from the two countries since the signing of the 1979 Egyptian-Israeli peace agreement.

"Regional cooperation has survived and proven itself," said Rep. Henry A. Waxman (D-Calif.), who sponsored legislation in 1979 that gave rise to the program.

The program is widely regarded in Egypt and Israel as the most productive forum for continuing contacts between scholars, scientists and officials. The two governments have had little success in developing any sustained cooperation in other fields.

The strains were apparent even at yesterday's opening session, where conference organizers said the nine scientists from Egypt preferred not to be quoted by name in the press to avoid possible adverse publicity in the Arab world.

The program's funding is now in danger of being cut back from $5.8 million to $2.89 million this fiscal year, according to an April 7 letter 28 congressmen sent to Secretary of State George P. Shultz protesting the administration decision.

"We do not understand this action," the congressmen said. "The program is the only component of our aid to Israel and Egypt aimed at building a long-term foundation of peace rather than simply providing a short-term payoff to the two governments.

"This is a fragile and sensitive time for Middle East peace. After a long period of backsliding after Camp David, Egypt and Israel may be moving forward. Scientists from several other moderate Arab nations have recently approached project participants about joining on a quiet, unpublicized basis," the congressmen said.

The scientific cooperation began in 1980 and has centered on infectious diseases, marine science and arid-land agriculture. Several projects in the social science field have been frozen because of the "cold peace" that began with the Israeli invasion of Lebanon in June 1982.

One of the projects has produced a new Middle East desert goat that produces more milk and meat and survives in a far drier environment than any previous species. The new breed is a cross between the Egyptian Barki goat, which lives in the Western Desert, and the "Damascus Goat" that is common in Syria, Turkey and Cyprus.

Egyptian and Israeli scientists have also grown a new shrub, or "salt bush," that Dov Pasternak, Israeli coordinator of the arid-land project, called a "breakthrough in desert agriculture." The shrub, whose Latin name is Atriplex Nummularia, is rich in protein and "very edible," according to Pasternak, who said it is already being planted in the Egyptian Western Desert and the Israeli Negev.

The scientists have also cross-bred fish to create a new high-protein species known as Sea Bream that will be served at a conference luncheon today at the Rayburn House Office Building. "It was more a question of trading of the data than the fish," said the American coordinator of the project, Robert B. Abel of the New Jersey Marine Science Consortium.

Another major success of Israeli-Egyptian scientific cooperation, according to conference organizers, was a joint effort to eradicate an epidemic in Egypt of leishmaniasis, a skin disease spread by sandflies, that broke out just after the start of the 1982 Israeli invasion of Lebanon.

Despite heightened tensions, Egyptian authorities took the risk of inviting Israelis to help battle the disease, "even bringing them into remote areas to work in the field," a conference report said. "Jointly, they controlled the outbreak," the report added.