A White House official said yesterday that "we're not in a position to take the Israelis fully at their word" that the Jonathan Jay Pollard spy case was an unauthorized operation "until the case is fully investigated."

The official said the White House is taking what he called "a middle ground" between the Justice and State departments, which are in conflict over the Pollard affair, and said the Reagan administration has reached no conclusions.

The official agreed with State Department arguments that there is no evidence to indicate widespread Israeli spying within the U.S. government, but said it also is "too early to absolve" the Israelis from the accusation. He agreed with Justice Department assertions that it was important to insist on full Israeli cooperation and to make every effort to see if Israeli spying extends beyond the Pollard case.

The White House official said the Israelis have cooperated in the Pollard case, and added that there are some officials in both the State and Justice departments who are "tending to draw premature conclusions" about an investigation that is continuing and has reached no findings.

Yesterday, amid heightening diplomatic tensions, a Defense Department official said the Navy has moved to tighten security procedures after the disclosures that Pollard, a former civilian Navy analyst, was able to remove stacks of classified military documents from his office complex without being searched.

Pollard, 31, pleaded guilty Wednesday to participating in an espionage conspiracy directed by Israeli officials in which Pollard was promised more than $300,000, prosecutors said.

The Israeli government has called Pollard's spying a "renegade" operation that functioned without the knowledge of top Israeli leaders. Justice Department officials have indicated that evidence gathered in its investigation raises questions about whether Israel has fully cooperated or tried to cover up crucial facts in the spy case, while State Department officials have said that Israel is cooperating fully and in good faith.

The White House official declined to estimate how long the investigation would last, but said the administration would continue to seek full cooperation from the Israelis as long as there were any questions outstanding.

White House officials acknowledged that the administration is walking a delicate political tightrope on this matter. President Reagan and his top aides have made it known they have confidence in the government of Prime Minister Shimon Peres and do not want to see it damaged by a widening spy scandal. At the same time, White House officials are concerned that the administration could be badly embarrassed if other Israeli spy operations were discovered.

"We want to be on top of the situation," a senior administration official said.

U.S. officials involved in diplomatic matters said the Peres government is becoming increasingly irritated with criticism here by some U.S. law enforcement officials that it has not fully cooperated.

Senior State Department officials, in acknowleging disagreements between the Justice and State departments over aspects of the Pollard case, said the dominant department position, which is shared by Secretary of State George P. Shultz, one of Israel's strongest supporters, is that Israel has kept its promise to cooperate.

These sources acknowledge that the circumstantial evidence presented by prosecutors -- that an Israeli air force colonel was Pollard's first alleged contact, that documents were copied in a specially equipped apartment here and that Pollard was promised $300,000 over 10 years in a Swiss bank account -- raise questions that the Israeli government knows more than it has admitted to and may have had a deeper role in recruiting Pollard and in subsequent attempts to cover up key facts.

However, these State Department sources stressed that, while some Justice officials are critical of the Israeli government, the investigation has so far failed to produce any evidence that proves Pollard conducted more than a "rogue" operation.

Last December, in publicly apologizing to the United States for the Pollard affair, Peres said that an internal Israeli inquiry had been launched to uncover all the facts "no matter where the trail may lead."

"I don't think anybody accused the Peres government of lying," said one U.S. official. "People have said they didn't do what they were supposed to do. They didn't try to find out what happened.

"Either they didn't want to find out or they already knew," the official said.

On the Navy's tightening of security, the Defense Department official declined to disclose specifics of the new procedures except to say that they will make it more difficult for Navy personnel to do what Pollard did.

Security procedures at the Navy, the Defense Department and other U.S. intelligence agencies have come under scrutiny in recent months in the wake of a series of much-publicized spy arrests. Last week, Ronald W. Pelton, a former $24,500-a-year communications specialist at the National Security Agency, was convicted of selling secrets to the Soviets in a case that a federal prosecutor said "may have caused the intelligence community more damage than any other turncoat in recent memory."

Pollard, while an analyst at the Naval Investigative Service's Anti-Terrorist Alert Center in Suitland, was able to obtain defense secrets outside his assigned area -- the Caribbean and the United States -- and from the offices of other defense-related intelligence agencies, including the Defense Intelligence Agency, according to federal prosecutors.

"A major part of this case is the screw-up in the internal security of the Navy and other repositories" of intelligence information, said a U.S. official familiar with the case.

Pollard, as part of his duties, had a "courier card" that enabled him to leave his office without being searched for classified documents that he was not authorized to have, prosecutors said.

"The procedures for all that have been changed radically," the Pentagon official said.

The official said that following Pollard's arrest last Nov. 21 outside the Israeli embassy here the department began an internal review of the Navy's handling of Pollard's top secret security clearances.

Another Defense Department source said last year that Pollard's security clearance was temporarily withdrawn in 1981 for "bizarre behavior." It was later restored, however, and Pollard also obtained access to "special compartmentalized information," which is higher than top secret.

The Pentagon official said yesterday he was unaware of the findings of the department's internal inquiry, which he believes is still under way.