Larry Franklin, 58, turned himself in on Wednesday, FBI spokeswoman Debra Weierman said.
He is scheduled to make an appearance in a US District Court in Alexandria, Virginia, later in the day, Weierman said.
The charge is the first in an investigation dating back to 2001 about whether Israel improperly obtained classified US information.
Franklin, who specialised on Iran and Middle Eastern affairs, allegedly gave the information to two people not entitled to receive it at a meeting in June 2003, FBI agent Catherine Hanna said in an affidavit.
The people at the lunch were employees of the American Israel Public Affairs Committee (AIPAC), a law-enforcement official said on condition of anonymity.
Franklin acknowledged at the lunch that the information was highly classified and asked that it not be used, Hanna said.
It concerned possible attacks against US troops by Iranian-backed groups in Iraq, the law-enforcement official said.
FBI agents twice searched AIPAC offices as part of the investigation. They also have interviewed two AIPAC employees about whether Franklin gave them classified information that wound up in Israel's hands.
The US and Israel are key allies
AIPAC said it gave the FBI files related to those same two employees, who previously were identified as Steve Rosen, the director of research, and Keith Weissman, deputy director of foreign-policy issues. Neither still works for the group.
AIPAC declined to comment on Wednesday, but has previously said it has done nothing wrong and is cooperating with the investigation.
The charge carries a maximum penalty of 10 years in prison.
A Pentagon official said Franklin continued to work at the Pentagon until his arrest.
However, Franklin's top-secret security clearance was suspended in June 2004, the Justice Department said. He formerly worked in the office of then undersecretary Douglas Feith.
The suspension followed a search of Franklin's West Virginia home that turned up 83 classified documents, Hanna said.
Jonathan Pollard was jailed in
1985 for spying for Israel
Franklin holds a doctorate in Asian studies and is a colonel in the Air Force Reserves.
The Israeli government has denied spying on the US, saying that meetings between US and Israeli officials are common and that the two countries share many secrets.
Information about Iran is of critical importance to Israel's security interests - particularly any assessments of its alleged nuclear ambitions.
Israel has said it has imposed a ban on espionage in the US since the scandal over Jonathan Pollard, an American caught spying for Israel in 1985.