A 25-year-old Palestinian was killed and 220 others wounded during the clashes on the Gaza Strip border, the Israeli media quoted the Gaza Health Ministry as saying.
It said some 8,000 Gazans had participated in the protests at five locations along the border. It marked the first time all members of the political bureau got together in Gaza, Hamas has said. Israel and Egypt imposed the blockade after the Islamic militant Hamas overran the territory in 2007.
United Nations officials have called for the blockade to be lifted, citing deteriorating humanitarian conditions in the Palestinian enclave run by Hamas where 80 percent of the two million population are dependent on aid.
"A number of suspects infiltrated into Israel from the southern Gaza Strip, hurled firebombs and an explosive device in the border fence area and then returned into the Gaza Strip", an army statement said.
The military said both vessels were taken to an Israeli port without incident.
Prime Minister Benjamin Netanyahu reportedly cancelled a planned visit to Columbia in order to be close to further possible developments in the truce negotiations. The ministry says that 159 Palestinians have been killed since the start of the "March of Return" protests on March 30.
Hamas has already hinted that it has not objected to the details of the agreement, but called for amendments, especially concerning a waterway linking the Gaza Strip with Egypt or Cyprus.
In a statement, Hamas spokesman Fawzi Barhoum said it included Marzouk, Rishq and Badran as well as Khalil al Hayya and Rawhi Mushtaha.
The Freedom Flotilla Coalition, an umbrella group for pro-Palestinian and Islamic charities from around the world, said Friday the Swedish-flagged vessel, Freedom, was almost 60 miles (95 kilometers) off the coast.
On Sunday, the Israeli navy intercepted a Norwegian-flagged activist boat that was part of the flotilla.
Hamas officials had no immediate comment on the ship's seizure.
The SY Freedom for Gaza was carrying mainly medical supplies and two of its passengers were journalists, said an organizer from a group named Ship to Gaza which organized the trip.