A senior al-Qaeda figure with close ties to the terrorist group’s current leader has left Iran, where he had lived for years after fleeing American forces in Afghanistan in 2001, according to former and current U.S. intelligence officials.

Thirwat Shihata is the latest terrorist suspect to leave Iran, raising questions about the country’s motives for allowing or forcing the departure of a string of al-Qaeda members that it had sheltered over the past decade.

U.S. officials said that Shihata, a 53-year-old Egyptian, was the deputy of Ayman al-Zawahiri, al-Qaeda’s current leader, when he ran Egyptian Islamic Jihad before it formally joined forces with Osama bin Laden in 1998.

“Shihata is among the few remaining members of al-Qaeda’s old guard,” said a U.S. counterterrorism official, who spoke on the condition of anonymity because of not having authorization to talk publicly about the movements of the al-Qaeda figures. “His ties to Zawahiri extend back decades, as both men cut their teeth in the Egyptian Islamic Jihad. . . . Shihata has kept a low profile in recent years, but there’s no question that he’s one of the more seasoned terrorists at large today.”

After the Sept. 11, 2001, attacks, dozens of al-Qaeda fighters, including some senior personnel, fled to Iran. It has never been clear how much freedom of movement they enjoyed while in the country, but for some the welcome appears to be over.

More on al-Qaeda in Iran

Get more details from the leaked top-secret 2008 document on al-Qaeda figures who went to Iran. Find out more.

In the past two years, up to a dozen notable figures have left Iran, and two — Nazih Abdul-Hamed al-Ruqai, accused in the 1998 East Africa embassy bombings, and Sulaiman Abu Ghaith, Osama bin Laden’s son-in-law and former spokesman — have subsequently ended up in U.S. custody.

A top-secret 2008 U.S. document, which was leaked by former National Security Agency contractor Edward Snowden, lists 13 senior al-Qaeda figures or associates in Iran. Five were listed as “senior management” in the terrorist group and of those, three have left Iran in recent years. Among them was Mahfouz Ould al-Walid, al-Qaeda’s ideological chief better known as Abu Hafs al-Mauritani, who returned to his native Mauritania in 2012.

The U.S. document describes Shihata as an “experienced operational planner” and “respected among al-Qaeda rank and file.”

[More details on the figures named in the 2008 document]

It was not clear when Shihata departed Iran, but a former U.S. official, who also requested anonymity, said he was believed to have traveled to Libya. The CIA declined to discuss Shihata’s whereabouts.

The former official said there was information that while in Libya in 2013, Shihata possibly met Ruqai, also known as Anas al-Libi, and Zubayr al-Maghrebi, another al-Qaeda figure who has left Iran.

U.S. forces captured Ruqai in Tripoli, Libya, in October and questioned him on a U.S. warship for days before moving him to New York to face trial on federal charges that he helped plan the bombing of the U.S. embassies in East Africa in 1998. Ghaith was arrested in Jordan while trying to connect to a flight to his native Kuwait, and he is also facing trial in New York on terrorism charges.

U.S. officials and counterterrorism experts are uncertain about the reason for the string of departures. “To me, it’s an enigma,” said Bruce Hoffman, a professor of security studies at Georgetown University.

Seth Jones, an analyst at the Rand Corp., said the relationship between al-Qaeda and Iran is difficult to unwind. At one point, the CIA had even talked to Iran about a trade, but it never went anywhere; in return for al-Qaeda suspects, Tehran would get some Iranian dissidents based in Iraq.

Jones said the Iranians might have lost an opportunity to capi­tal­ize on their high-value guests.

“I think the strategic rationale for keeping them has decreased over time,” he said. Officials also speculate that the civil war in Syria, where the Iranian government and al-Qaeda are on opposite sides, may have strained relations to the point that the government in Tehran is no longer willing to harbor these fugitives.

In the release of a small portion of the cache of documents taken from bin Laden’s compound in Pakistan, the former leader of al-Qaeda speculated that Iran freed some from detention after al-Qaeda kidnapped an Iranian diplomat.

Not much is publicly known about Shihata. He had ties to an alleged terrorist in Canada who was suspected of serving as “a communications conduit for terrorist cells” that carried out the Africa bombings,” according to a diplomatic cable released by the anti-secrecy group WikiLeaks.

In 2011, Shihata issued a statement backing the overthrow of Egyptian President Hosni Mubarak, according to the Long War Journal. He issued the statement from Iran.