NEW YORK (Reuters) - A former spokesman for al Qaeda says he was the subject of an extrajudicial transfer to U.S. custody via three Middle Eastern countries this year, an allegation that suggests President Barack Obama's administration is still carrying out controversial "rendition" operations.

Suleiman Abu Ghaith, a close associate and son-in-law of Osama bin Laden, was victim of "an absolute rendition ... an extrajudicial rendition," said Stanley Cohen, a New York lawyer who is representing Abu Ghaith.

The Kuwaiti cleric has pleaded not guilty in Federal Court in Manhattan to charges of conspiring to kill Americans.

The use of "rendition" was a counterterrorism tactic begun under President George W. Bush when suspected al Qaeda figures were grabbed by CIA teams around the world and transferred without judicial process to third countries or to secret prisons that the U.S. spy agency maintained overseas.

When he came to office in 2009, Obama renounced so-called enhanced interrogation techniques, which human rights advocates and some U.S. politicians have described as torture. But his administration said it would not completely ban the use of rendition.

In the first trial of its kind against "rendition" flights, an Italian judge in 2009 sentenced 23 Americans in absentia for the abduction of an Egyptian Muslim cleric who was snatched in Milan in 2003 and sent to Egypt. Former CIA Milan station chief Robert Seldon Lady, given a nine-year prison sentence, was detained in Panama this week, and the State Department said on Friday he was headed to the United States.

Abu Ghaith, who was a spokesman for al Qaeda around September 2001, is one of the highest-ranking al Qaeda figures to face U.S. criminal charges for crimes related to the September 11 attacks. He has pleaded not guilty to charges of conspiring to kill Americans, and faces a January 2014 trial.

In a court affidavit filed on Friday, Abu Ghaith confirms that after the attacks he fled to Iran, where he was arrested in mid-2002.

He claims he was held without charge in different prisons in Iran until January 2013. Iranian authorities periodically interrogated him, he says, and they also advised him that the U.S. government was aware he was in their custody.

Abu Ghaith says that on January 11, the Iranian government informed him he was being released and allowed him to enter Turkey, where he believed he would be allowed to return to his native Kuwait.

However, within 12 hours, Turkish authorities arrested him, he says. After about 45 days of interrogation by Turkish authorities in Ankara, Abu Ghaith says, he was put on a plane and told that he would be flown to Kuwait.

Instead of flying to Kuwait, Abu Ghaith says, his plane landed in Amman where he was handcuffed and hooded by Jordanian police and handed over to a group of people who he believed included Americans.

Later, this group re-shackled Abu Ghaith and replaced his hood with blacked-out goggles, earplugs and noise-proof headphones, he says. Then he was put on a plane, and once airborne he was introduced to a man who identified himself as being from the FBI. Upon landing in New York, he was taken to Manhattan and imprisoned to await trial.

U.S. authorities have said that over the years, they were aware of the presence in Iran of Abu Ghaith and other al Qaeda figures, including a top aide to bin Laden and one of the al Qaeda leader's sons.

(Reporting by Mark Hosenball and Bernard Vaughan; Editing by Alistair Bell and Mohammad Zargham)

[An artist sketch shows Suleiman Abu Ghaith, a militant who appeared in videos as a spokesman for al Qaeda after the September 11, 2001 attacks, appearing at the U.S. District Court in Manhattan March 8, 2013. REUTERS/Jane Rosenberg]