"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.
The army said some 8,000 people took part in five separate protests along the border, and that troops responded with riot disposal means and live fire in accordance with appropriate rules of engagement.
The organisers of the flotilla said the boat, which was carrying medical supplies, was intercepted in worldwide waters.
"Ship to Gaza demands that those who have been taken prisoner and the ship and its cargo are returned to the location where the ship was boarded and are allowed to continue their journey in global and Palestinian waters unmolested, in accordance with worldwide law", the group said in a statement.
An unnamed Israeli official said Sunday that there might be talks focusing on a proposal to ease the blockade of Gaza if the Palestinians calm their side of the fence that separates the occupied territories from the blockaded coastal sliver.
Ahmed al-Ayeda, 17, was shot on March 30 - the first day of months of protests and clashes along the border - the ministry said in a statement late Sunday.
A member of the Israeli Security Cabinet, Ze'ev Elkin (Likud), referred to the ceasefire talks with Palestinian resistance movement Hamas and said that "an arrangement with the organization is now not on the agenda". Yaghi and Suri were buried on Saturday.
There are more than 4000 fishers and around 700 boats in the Gaza Strip providing livelihood to at least 70.000 Palestinians, while the Israeli military and navy keep attacking them, kidnapping them and confiscating their boats, in addition to the dozens of casualties, including fatalities, resulting from these violations.
The protests have also seen Palestinians fly airborne incendiary devices toward Israeli territory, sparking hundreds of fires in southern Israel and causing millions of shekels in estimated damages.
According to medical sources, one of the wounded was a boy.
With borders to both Egypt and Israel largely sealed in recent years, Gaza suffers from desperately high rates of poverty and unemployment.
An unnamed Israeli official was quoted by a number of media outlets as saying that Israel will not accept a broad agreement with Hamas on the rehabilitation of the Gaza Strip which does not include the return of the remains of IDF soldiers Hadar Goldin and Oron Shaul and the two Israeli citizens held by the terror group.
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