The flotilla was making a renewed attempt to deliver aid to Gaza on Tuesday after earlier missions were intercepted by Israel in international waters.
Video from the flotilla's livestream showed soldiers firing shots at two of the boats. The type of ammunition fired was not clear.
"At no point was live ammunition fired," the Israeli foreign ministry said in a statement.
"Following multiple warnings, non-lethal means were employed toward the vessels - not toward protesters - as a warning. No protesters were injured during these events," it added.
The Global Sumud Flotilla later said that all 50 boats in the flotilla had been intercepted in the eastern Mediterranean, with 428 participants from more than 40 countries detained, including 78 Turks.
Israel's foreign ministry said all 430 activists had been transferred to Israeli vessels and were en route to Israel. It said the activists would be allowed to meet their consular representatives.
It was not immediately clear why Israel and the flotilla offered differing numbers for those on board.
The foreign ministry had said on X on Monday that it "will not allow any breach of the lawful naval blockade on Gaza".
Speaking in Ankara late on Monday, Turkish President Tayyip Erdogan condemned the intervention against the "voyagers of hope" in the flotilla and called on the international community to act against Israel's actions.
Ships from the Global Sumud Flotilla had set sail for a third time on Thursday from southern Turkey, after earlier attempts to deliver aid to Gaza were intercepted by Israel in international waters.
The group said previously there were 426 people taking part in the flotilla from 39 countries.
The US Treasury said on Tuesday it was imposing sanctions against four people associated with what it described as the "pro-Hamas" flotilla.
Pro-Palestinian activists say Israel and the US wrongly conflate their advocacy for Palestinian rights with support for Hamas militants.
Palestinians and international aid bodies say supplies reaching Gaza are still insufficient, despite a ceasefire agreed in October that included guarantees of increased aid.
Most of Gaza's more than two million people have been displaced, many now living in bombed-out homes and makeshift tents pitched on open ground, roadsides, or atop the ruins of destroyed buildings.
Israel, which controls all access to the Gaza Strip, denies withholding supplies for its residents.
