BAGHDAD, Aug 10 (Reuters) - Powerful Iraqi Shi'ite cleric Moqtada al-Sadr is in Iran and not in complete control of the militia that owe allegiance to him, the U.S. commander in Sadr's main stronghold in Baghdad said on Friday.

"I think he is now in Iran so just based on his location that implies that some of his control is not direct," Colonel John Castles said in a video conference from Baghdad with journalists in Washington.

Castles is in command of U.S. forces responsible for Sadr City, the vast Shi'ite slum named for Sadr's father who was killed under Saddam Hussein and now the young cleric's main power base in the capital.

A spokesman for Sadr's office in the Shi'ite holy city of Najaf denied that the cleric had left the country.

"Moqtada al-Sadr is in Najaf and has never left," the spokesman said.

Sadr was last seen in public in Iraq attending a religious ceremony in the holy city of Kufa on May 25, when he denounced the United States as part of an "evil trio" with Britain and Israel.

U.S. officials said at the time that they believed Sadr had been out of the country for the previous four months, and they said in July they believed he had left Iraq again.

Castles said civilian branches of Sadr's office in Sadr City still have influence over the 2 million Shi'ites living there, but it was no longer clear how much control the cleric had over the armed wing of his followers, the feared Mehdi Army militia.

"I think he certainly exudes some influence just by the fact that the office of Moqtada al-Sadr is very strong in Sadr City and he has a direct influence over that," he said.

"In relation to the Mehdi Army though, it's hard to tell. I personally think it's fractured somewhat, that they don't get a whole lot of direct guidelines from him and that some of these divisions of it are operating on their own," Castles said.

U.S. commanders said this week that nearly three quarters of attacks against their troops were now coming from Shi'ite militants, many believed to have links to Iran.

On Wednesday, U.S. forces said they killed 30 Shi'ite militants in an air strike during a raid in Sadr City. Hospital sources put the death toll at 13, including at least one woman. (Reporting by Khaled Farhan in Najaf and Kristin Roberts in Washington)

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