The 27-page document, which is still under court seal, provides an extraordinary look at what the agents considered to be espionage activity in a nearly five-year counterintelligence probe of one of the pro-Israel lobby’s top officials.

It also shows that the everyday activities of diplomats, lobbyists and reporters — namely, meeting with U.S. officials, taking notes and then trading that information with other officials — was considered spying by the bureau.

In addition, the AIPAC investigation has had a lasting effect on U.S.–Israel relations: The FBI blocked Israel‘s current national security adviser from entering the United States between 2007 and 2009 on grounds that he had met with a secondary target of the probe.

According to the search warrant affidavit, agents thought Steven J. Rosen, then-director of foreign-policy issues for AIPAC, was collecting classified U.S. information from government officials and passing it on to American reporters and Israeli officials.

“Based upon my training and experience as an counterintelligence investigator, I believe Rosen is collecting U.S. government sensitive and classified information, not only as part of his employment at AIPAC, but as an agent of Country 1,” FBI agent Eric Lurie wrote in the affidavit.

Country 1 refers to Israel, according to law enforcement officials familiar with the investigation.

However, Mr. Rosen, who pioneered AIPAC‘s practice of lobbying the executive branch in the early 1980s, was never charged with being a spy.

The probe resulted in only one conviction: Lawrence A. Franklin, a Pentagon analyst whom the FBI coaxed into offering Mr. Rosen and his AIPAC colleague, Keith Weissman, classified data about Iran as part of a sting. Franklin pleaded guilty in 2006 to three counts of mishandling classified information.

The case highlights caution-taking and suspicion-inducing aspects of the spy-vs.-spy intelligence community, even among allies who routinely share intelligence, as the U.S. and Israel do.

Among the potential crimes Mr. Lurie focused on in the search warrant affidavit was a section of the Espionage Act dealing with “gathering or delivering defense information to aid a foreign government.”

The list of items to be seized included “safety deposit box records, including signature cards, bills and payment records” and “any and all copies of classified documents, books, reports, photographic negatives, blueprints, plans, maps, models and notes,” according to the warrant.

Those items were not found, but the warrant says that an earlier, unannounced FBI inspection of Mr. Rosen‘s office found three classified documents.

In a recent interview, Mr. Rosen told The Times that the FBI‘s claim about the documents was false. The documents discussed in the warrant were academic papers the CIA sent him as preparation for a conference he attended. “The CIA sent me those documents at their own behest,” he said.

The CIA declined to comment for this report.

“I was not getting classified documents,” said Mr. Rosen, who is suing AIPAC for defamation. “The FBI followed me around for five years, they searched my office and searched my home, and they never found any classified documents, because there were none to find.”

U.S. Attorney Paul McNulty eventually charged Mr. Rosen and Mr. Weissman with conspiring to disclose defense information, or leaking.

But Mr. McNulty dropped those charges in 2009 after civil liberties groups argued that the prosecution set a precedent of indicting private citizens who did not hold security clearances for leaking. To date, only U.S. officials who hold security clearances have been convicted under the anti-leak provisions of the espionage statute.

More important, the prosecuting attorneys during pretrial motions acknowledged that the AIPAC officials were not acting as agents of a foreign power.

“The fact that the defendants were not agents of Israel, or any foreign nation, does not negate any element of the offense, and cannot be exculpatory,” the U.S. attorneys wrote in a 2006 response to motions from the defendants in the case.

FBI spokesman Paul Bresson said in response to queries about the AIPAC investigation: “The FBI is charged with following through on all investigative leads, and we would have done so in this case whether or not they resulted in prosecutive action.”

The FBI search warrant describes what it stated was Mr. Rosen‘s pattern of collecting information through routine meetings with U.S. government officials, reporters and Israeli diplomats — activities that scores of lobbyists, activists, diplomats, analysts and journalists engage in every day in Washington.

“Rosen uses his contacts within the United States government to obtain classified United States government information, which he in turn passes on to officials from a foreign government (Country 1), members of the media and other persons not authorized to receive classified information in an effort to influence United States government policies and benefit Country 1,” according to the affidavit.

“I worked for a pro-Israel organization that very openly maintains relations with the Embassy of Israel,” Mr. Rosen said. “All of these officials knew very well I met with members of the Israeli Embassy. The U.S. government considered openly that we were in a kind of triangle with the Israeli government.

“It was part of the work, as I am sure it is today part of the work for AIPAC officials.”

For decades, the federal government has at times looked into AIPAC, a lobby that is composed of U.S. citizens who advocate for closer ties between the U.S. and Israel.

AIPAC spokesman Patrick Dorton said in a statement: “Any suggestion that any AIPAC employee has ever been an agent of a foreign power is patently false. AIPAC is an American organization that represents American citizens and advocates for American interests.”

Nonetheless, the FBI has been suspicious. Morris Amitay, AIPAC‘s executive director from 1974 to 1980, said that when he headed the organization, “two agents from the Department of Justice showed up unannounced and said they were investigating whether AIPAC should register as a foreign agent, as opposed to a domestic foreign-lobbying organization.”

Mr. Amitay said: “I invited them to look at all of our records and to speak to any employee they wished, but I assured them that, as an attorney myself, I was conversant with the Foreign Agents Registration Act and that AIPAC was scrupulous to avoid crossing any line to have to register as foreign agents.”

In addition, the FBI blocked Uzi Arad, the current Israeli national security adviser, from entering the country between 2007 and 2009 on grounds that he met with Franklin in 2002.

No friends in intelligence

Among the crimes the affidavit says there was probable cause to suspect Mr. Rosen had committed was a failure to register with the attorney general as an agent of a foreign power.

The scrutiny of AIPAC corresponds with overall scrutiny of Israel‘s intelligence-gathering in the United States.

Israeli officials have said publicly they do not target the United States in intelligence activities. Ilan Mizrahi, a former deputy chief of Israel‘s Mossad intelligence agency, said recently that Israel did not spy on the United States. “This is a taboo. It was a taboo always, not only against the United States, but also in other friendly countries,” he said.

Current and former U.S. counterintelligence officials say the Israelis are considered a cyberthreat to U.S. government networks, along with allies like France and India and adversaries like China, in that Israeli hackers have probed U.S. networks for vulnerabilities and means to monitor sensitive traffic.

“Israel, India and France have substantial cyber-intelligence-gathering capabilities,” said Stewart Baker, a former general counsel for the National Security Agency and Department of Homeland Security. “Because you have no friends in the intelligence world, you have to judge countries in part by their capabilities, not by whether you are getting along today.”

Also, Israeli technology firms have long been suspected of trying to steal trade secrets from U.S. companies, something suspected of European companies as well. In the 1980s and 1990s, the Pentagon locked horns with Israel over the retransfer of defense technology to China.

“Israeli companies have been aggressive in attempting to obtain technology transfer. There have been a number of cases of industrial espionage involving Israeli companies,” said Oliver “Buck” Revell, a former associate director of the FBI who oversaw counterintelligence investigations at the bureau.

Another factor that has led counterintelligence officials to suspect Israeli intelligence-gathering is the case of Jonathan Pollard, who sold U.S. secrets to the Israelis while he served as a Navy intelligence analyst 25 years ago. He is serving a life sentence in a federal prison in North Carolina.

This month, Israeli Prime Minister Benjamin Netanyahu made a public plea for Pollard‘s release before the Knesset, Israel’s parliament. U.S. Jewish organizations on the same day signed a letter, along with other religious leaders, asking that Pollard, 56, be released.

Abe Foxman, national director of the Anti-Defamation League, said the scrutiny of Mr. Rosen reflects the belief among some in the intelligence community that Pollard must have worked with someone else, because much of the intelligence he stole was not related to his areas of expertise.

“I believe this goes back to this notion that there was a second Pollard and it was bigger than Pollard,” Mr. Foxman said. “I am not sure that to this day they have given up this fantasy notion. I would rather they pursue this, come up with nothing, rather than not be given the opportunity to pursue it and saying, ‘if only they let us, we would find something.'”

Mr. Revell said the U.S. government had a “rather vigorous discussion with the Israelis” after the Pollard arrest. He added that he considers the Pollard affair to be a “one-off” event and not part of a pattern of Israelis recruiting Americans. He also said there were no ties that turned up connecting Pollard to pro-Israel groups such as AIPAC.

“We do not consider the Israelis a national security threat to the United States,” Mr. Revell said. “What we do want to do is to make sure that some individual entities or individuals do not become overzealous, that in their desire to help Israel do not cross the line and take actions that are detrimental to U.S. security or intelligence.”

Mr. Revell said he was talking about times in which the Israelis had disclosed intelligence that was shared discreetly. “Even with your friends, you have to say at times, ‘You are going too far.'”