There is evidence that Israel has run intelligence operations in the United States for years, despite Israeli assertions that the Jonathan Jay Pollard spy case was an isolated episode, according to current and former U.S. intelligence officials.

Israeli intelligence services were "more active than anyone but the KGB . . . . They were targeted on the United States about half the time and on Arab countries about half the time," John Davitt, longtime head of the Justice Department's internal security section until his retirement in 1980, said in a recent telephone interview.

Davitt, who was responsible for reviewing all espionage cases pending at the Justice Department, said he recalled a handful of cases during his 30 years of government service in which Israeli diplomats suspected of espionage were quietly asked to leave the United States.

A secret 1979 Central Intelligence Agency document on Israel's "Foreign Intelligence and Security Services" noted that two of Israel's first three intelligence priorities involve the United States. The Arab states were the first targets listed. Second was "collection of information on secret U.S. policy or decisions, if any, concerning Israel." Third was "collection of scientific intelligence in the United States and other developed countries."

Other U.S. intelligence officials, who declined to be identified, said they were aware of a number of cases of Israeli intelligence operations in the United States. Some involved leaks of classified information to Israeli agents by Americans who were pro-Israel but were not paid agents like Pollard.

Israeli Embassy spokesman Yossi Gal last night reiterated an earlier statement that the "Pollard affair was an unauthorized deviation from the clearcut Israeli policy of not conducting any espionage activity whatsoever in the United States . . . . "

One previously unpublicized example of Israeli activities apparently involved Rafael Eitan, the longtime Israeli intelligence official named yesterday in court papers as Pollard's chief handler. Eitan's name appears in a U.S. government document contained in a file about a case in the 1960s involving uranium, which disappeared from a Pennsylvania plant and has long been suspected of being diverted to Israel for use in an atomic bomb.

A declassified Federal Bureau of Investigation document shows that a "Raphael Eitan, chemist, Ministry of Defense, Israel, born 11/23/26, in Israel" was part of a four-man Israeli team that asked to travel to the NUMEC uranium processing plant in Apollo, Pa., in September 1968. The Washington Post has learned reliably that the Eitan named in the Pollard case has the same birthdate.

Eitan was a participant in the Israeli kidnaping of Nazi war criminal Adolf Eichmann from a Buenos Aires street in 1960, according to Israeli sources. In 1968, he reportedly was an officer of the Mossad, the Israeli intelligence service. More recently, he has served two Israeli prime ministers as adviser on terrorism.

During the 1960s, the FBI investigated NUMEC's founder, a U.S. nuclear scientist named Zalman M. Shapiro, because inspections by the Atomic Energy Commission found that 200 pounds of enriched uranium -- enough to make six atom bombs -- were missing from his plant near Pittsburgh, according to previously declassified government files. U.S. officials believe the uranium had disappeared by the mid-1960s; Shapiro denied that he gave the uranium to the Israelis and the case was closed with no charges being filed.

Shapiro could not be reached for comment yesterday. His sister, Mrs. Zipporah Schefrin, said he was hospitalized following recent surgery. Eitan, who now heads a state-owned chemical plant, did not return phone calls in Israel.

Eitan was scheduled to be accompanied to the NUMEC plant in the fall of 1968 by Avraham Hermoni, the scientific counselor at the Israeli Embassy, and by two men identified as being from Israel's Department of Electronics, according to the FBI document made public under the Freedom of Information Act. It is unclear whether the trip ever took place.

Diplomatic lists show that Hermoni was scientific counselor at the Israeli Embassy from 1968 to 1972. Officials at the Israeli Foreign Ministry and the Ministry of Science and Development, which has a Department of Electronics, said yesterday that they did not know any of the names listed in the 1968 FBI document.

Sources familiar with the NUMEC case said the FBI learned of a meeting which Hermoni attended at Shapiro's house with 11 American scientists in November 1968, two months after the planned trip to NUMEC. In June 1969, the sources added, FBI agents watched Shapiro meet in the Pittsburgh airport with another scientific attache from the Israeli Embassy.

Scientific attaches have been identified as contacts in a number of suspected cases of Israeli espionage over the years, according to one knowledgeable federal law enforcement source. One of Pollard's handlers was a science consul at the Israeli consulate in New York. An earlier case involved another U.S. Navy employe, who was investigated in the early 1970s but not prosecuted, the law enforcement source added.

Other intelligence and diplomatic sources, however, also noted that Israel and the United States have had a long tradition of sharing intelligence, such as recent cooperative efforts to combat terrorism.

In another case, declassified documents show that Davitt's staff recommended in 1979 that a grand jury investigate allegations that Stephen D. Bryen, who had been a member of the Senate Foreign Relations Committee staff, had given secrets to Israeli Embassy officials. The recommendation was rejected by superiors. Bryen, who strongly denied the charges, is now a Pentagon official responsible for reviewing which U.S. technology may be exported.

A series of investigations of the NUMEC case has fueled speculation about Israel's nuclear weapons capability. The latest episode was in May 1985, when Richard K. Smyth, a California businessman, was indicted by a federal grand jury for illegally shipping to Israel 810 "krytrons," electronic devices that can be used in the triggers of nuclear weapons. Smyth fled the country after he was indicted. At the time Israeli government officials said some of the krytrons had been used for nonnuclear purposes and promised to return those that were unused.

Recent public disclosures show that the CIA believed Israel had an atomic bomb as early as 1968.

The CIA drafted a National Intelligence Estimate on the Israelis' nuclear capability in 1969, but Carl Duckett, who was head of the agency's directorate of science and technology, said that then-CIA Director Richard M. Helms told him not to publish it, according to government documents.

According to Duckett's account, President Lyndon B. Johnson told Helms, "Don't tell anyone else, even Dean Rusk and Robert McNamara," then secretaries of state and defense respectively. Helms has said he has no recollection of such a conversation with Duckett.

By 1974, according to another CIA document on nuclear proliferation inadvertently made public, the agency had concluded: "We believe Israel already has produced nuclear weapons. Our judgment is based on Israeli acquisition of large quantities of uranium, partly by clandestine means . . . . "