A Europe-bound boat carrying 17 passengers, some of whom were injured in recent clashes with Israeli forces, has been captured a short distance from the Gaza port.
The Israeli military has intercepted a Palestinian protest bound for Limassol in Cyprus.
The Freedom Flotilla set sail from the local port on Tuesday in defiance of a 12-year Israeli sea blockade on Gaza.
The boat, said to be carrying 17 passengers and crew, was stopped by the Israeli navy which announced it had taken control of the vessel less than 12 miles from its home port.
The International Freedom Flotilla Coalition (FFC) said in a statement it "condemns Israel's brutal act of state piracy in attacking the aptly named Hurriya (Liberty) vessel which attempted to leave the port of Gaza today filled with people needing urgent medical assistance as well as students and crew, as they attempted to peacefully make safe passage to Cyprus.
"This latest attempt to break the illegal blockade of Gaza continues the brave challenges during the Great March of Return, where more than 120 Palestinians have been shot and killed by Israeli snipers and thousands severely injured."
Palestinian student, Ihab Abu Armana said: "Our message is a humanitarian message. The world must know that on the land of Gaza there are people who deserve life - young and old, sick and disabled, students and graduates. The siege on us for 12 years must be broken. We are a people who deserve to live."
One of the patients on board, Kama Al Tarazy, said: "God willing we can leave for Europe to get health treatment. We are asking the international community to protect the injured and the sick people on these boats."
The International Freedom Flotilla Coalition said it was attempting to end the blockade of Gaza.
The move is likely to increase tensions after mortar fire from the enclave earlier in the day, and weeks of deadly unrest.
It comes as Israel carried out strikes against militant bases in the Gaza Strip following a barrage of mortar fire from the Palestinian enclave.