The protests on Friday occurred a day after a senior Hamas delegation arrived in the Gaza Strip from Egypt to discuss a possible cease-fire with Israel and resume internal reconciliation with Palestinian President Mahmoud Abbas' Fatah Party.
It was the latest in a series of protests along Gaza's perimeter fence with Israel, aimed in part at trying to break an 11-year-old border blockade.
With borders to both Egypt and Israel largely sealed in recent years, Gaza suffers from desperately high rates of poverty and unemployment.
Separately, Israel's prime minister has put off a planned South America trip and called a special Cabinet meeting Sunday to monitor Gaza developments.
On Friday Ezzat al-Rishaq, a member of the Hamas political office, told protesters along the border they were "committed to calm".
The 'Freedom, ' a boat headed to the Gaza Strip in a flotilla defying Israel's blockade.
In a statement, the Israeli military said the vessel was carrying 12 people and had been taken to the port of Ashdod. Israel shelled a Hamas post in response.
More than 140 Palestinians have been killed by Israeli forces since the outbreak of the Gaza border protests on March 30. Others, among them armed Hamas militants, have been killed in attempted border attacks or in Israeli airstrikes.
In one area east of Gaza City, protesters burned tires, releasing thick plumes of black smoke.
His return to Gaza has been interpreted in Israeli and Palestinian media as "relevant to negotiations through third parties for a long-term agreement between Hamas and Israel". 130 other protestors were also wounded, but not directly from live ammunition.
Ship to Gaza, the organisers of the flotilla, said the boat was carrying medical supplies and was intercepted in global waters late on Friday.
Birawi stressed that numerous activists rejected voluntarily deportation, preferring to delay it for more than 72 hours, the legal deadline for accepting voluntary deportation from the country, in order to appear before an Israeli court to expose the unjust practices of Israeli naval forces who attacked the humanitarian ship in worldwide waters, and to later prosecute Israel for its actions.