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The indictment against Mr. Franklin makes two references to “a person previously associated with an intelligence agency of [foreign official’s] country.” Two former U.S. officials and a former Israeli official have confirmed that Mr. Arad is the “person.”

The passage refers to a meeting between Mr. Franklin and Mr. Arad on Feb. 20, 2004, at the Pentagon cafeteria and an earlier recommendation by an Israeli diplomat that Mr. Franklin meet with Mr. Arad.

In his letter, Mr. Reichman referenced the section of the Immigration and Nationality Act that deals with espionage issues, saying, “it being absolutely certain to me and to all who know him, that none of the causes specified … apply to him.”

A Washington immigration lawyer, Glen Wasserstein, said Mr. Arad was being barred under the section of law that “allows the government to deny entry to those foreign nationals it deems as spies or saboteurs, and those who help or assist in such spying or sabotage.”

Mr. Wasserstein said the president or attorney general could waive the restriction on the visa.

Buck Revell, a former associate director of the FBI who oversaw counterintelligence investigations at the bureau, added that as national security adviser, Mr. Arad would not be in a position to engage in espionage or intelligence activities.

Nonetheless, Mr. Revell said, the suspicion surrounding Mr. Arad could hamper U.S.-Israel relations.

“The [Israeli] national security council chairman has access to all of Israel’s intelligence and all the intelligence we share with them, normally,” Mr. Revell said. “Whether or not our agencies would restrict any type of intelligence from going to him would be very problematic. That is something they will have to deal with.”

A senior official of the incoming Netanyahu administration, who spoke on the condition that he not be named because of the sensitivity of the issue, told The Times that he expects Mr. Arad to be able to travel to the United States for official business.

“This is an issue that the new government of Israel trusts can be resolved,” the official said.