Flotilla organiser Claude Leostic said that when the "Dignité Al Karama" stopped to refuel at a port in Crete, it was taken to nearby Sitia and that the authorities were "stopping the boat from setting sail for various administrative reasons."
The boat had left the Greek port early on Tuesday in defiance of a ban on any ships setting sail from Greece with the intention of running the Israeli blockade on Gaza.
All the other boats which hoped to participate in the 10-vessel international flotilla to Gaza, have been prevented from leaving ports in Greece, while an Irish boat, which organisers say was sabotaged, is under repair in Turkey.
Officials in Athens say they imposed the ban for the safety of the activists on board, after Israeli commandos boarded a similar flotilla last year, and 9 Turkish activists were killed in the ensuing violence.
Organisers this year say that Greece has been pressured by Israel to impose administrative obstacles.