Greek authorities Saturday arrested John Klusmire, 60, captain of the Audacity of Hope, which was to carry American activists as part of the "freedom flotilla."
He could have faced a possible year in jail pending trial on charges of endangering the safety of his passengers by sailing without permission.
The boat is still impounded at a military dock near Piraeus, the port of Athens.
"The charges were ridiculous," said Jane Hirschman, a spokeswoman from the U.S. contingent. "All this confirms the far-reaching tentacles of the Israeli state."
Meanwhile, one boat in the flotilla, a small French vessel carrying seven activists and a journalist, slipped out of Greek waters overnight, evading the coast guard. Organizers announced the sailing after the craft reached international waters.
Adam Shapiro told The New York Times it was unclear whether the boat had enough fuel to reach Gaza.
"It's kind of in a holding pattern for the moment," he said. "We're trying to find out what is the next step."
On Monday, the activists rejected a Greek offer to deliver the humanitarian aid to Gaza.