Israeli aircraft destroyed a boat moored in Gaza city early on Wednesday morning, local residents said. There were no reports of casualties.
The Israeli military said aircraft had struck "military targets belonging to the Hamas terror organisation's naval force" and "underground terror infrastructure" in the northern Gaza Strip.
The military said the air strikes were carried out in response to an incident on Tuesday when a group of men from Gaza broke through the border fence into Israel and set fire to an army post. An Israeli tank then targeted a Hamas observation post. No casualties were reported.
Gaza residents said the vessel that was hit by missiles was set ablaze. They said it was due to sail to meet a flotilla of boats hoping to reach Gaza. Israel maintains a naval blockade of the Gaza Strip and has in the past stopped other boats from reaching its shores.
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Arab states must unite to alleviate Palestinian suffering
Violence along the Israel-Gaza border reached a peak on May 14 when Gaza medical sources said at least 60 Palestinian protesters were killed by Israeli gunfire. It has subsided but there are sporadic flare-ups.
Since the border protests began on March 30, 110 Palestinians have been killed, Gaza medical officials said.
Gaza has been controlled since 2007 by Hamas. Israel and Egypt, citing security concerns, maintain a de facto blockade on Gaza, which has reduced its economy to a state of collapse.
Two million Palestinians live in the narrow strip, most descendants of refugees who fled or were driven out of homes during fighting between Jewish and Arab forces at the time Israel was founded.