The Al-Qassam Brigades, the armed wing of Hamas, issued a statement denouncing the Israeli assassination of two of its fighters, in northern Gaza, and holding Israel accountable for any future escalation.
Local witnesses confirmed that the Israeli artillery fired two shells targeting a Hamas military post in northern Gaza killing two Palestinians.
The military said the tank responded to shots fired at soldiers from the post.
"The (military) clarified to the ship's passengers that they are violating the legal naval blockade and that any humanitarian merchandise can be transferred to Gaza through the Port of Ashdod", the statement said.
A high-level delegation from Hamas has also arrived in Gaza Strip since on Thursday after talks with Egyptian officials.
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About 158 Palestinians have been killed and more than 17,000 others injured by Israeli gunfire during the rallies, which take place every Friday.
Israel accuses the Islamist Hamas movement, which has been controlling the coastal enclave since 2007, of using the protests as a cover to damage the border fence, infiltrate the Israeli territory and launch attacks.
United Nations and Egyptian-led efforts are under way to mediate a long-term truce between Israel and Hamas that would end a four-month upsurge of violence along the Israel-Gaza border.
Israel's security cabinet discussed the proposal on Sunday, but afterwards ministers said only that the Israeli military was "prepared for any scenario".