Captain John Klusmer was arrested when the US boat Audacity of Hope -- the flagship in a flotilla of pro-Palestinian activists -- attempted to leave Greek waters on Friday after Athens banned all Gaza-bound ships from setting sail.

Klusmer was charged with a felony and ordered to appear in court on Tuesday. The US Boat to Gaza organisation said he was being held in jail in "shocking conditions" and as far as it was aware, had not yet received consular assistance.

New York lawyer Richard Levy -- a passenger on the boat who has visited Klusmer in jail in a port town near Athens -- told enraged US activists that "he had no bed or toilet in his cell, and is receiving no food or water."

"We've offered to pay his bail," said passenger Robert Naiman, from the Washington-based Just Foreign Policy organisation. "But we have had no indication at all that he will be allowed out of jail before Tuesday."

The US Embassy in Athens was not available for comment.

The Audacity of Hope -- which was carrying 3,000 letters of support for Palestinians -- set sail without warning, leaving behind nine other ships that had hoped to sail together to challenge Israel's naval blockade on Gaza.

It was quickly intercepted by a coastguard vessel with masked, armed men on board. After a two-hour stand-off, the boat turned back to a small naval port.

Passengers were free to go but initially chose to stay on board in defiance of the Greek authorities.

Sunday morning they were back in Athens to "do what we can do help the captain," including "reaching out to members of the US Congress" for help in getting Klusmer released or improving the conditions in which he is held.

The flotilla has been beset with bureaucratic problems and two cases of "sabotage" over the last week and only four of the initial 10 boats were in the running Sunday for another attempt to defy the Greek ban and set sail.

Israel credited its "diplomatic efforts" for the delays and setbacks that have kept the vessels grounded. "I welcome all the efforts that have been made to stop the flotilla," Foreign Minister Avigdor Lieberman Lieberman said Sunday.

"The success... is the fruit of intensive contacts with states in the region and the international community," he said.

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