The flotilla was making a renewed attempt to deliver aid to war-shattered Gaza after earlier missions were also intercepted by Israel in international waters.
Video showed Israeli forces opening fire on at least two flotilla vessels on Tuesday, with Israel saying those were warning shots.
Organisers say they aim to break Israel's blockade of Gaza by delivering humanitarian assistance, something aid bodies say is still in short supply despite a US-brokered ceasefire between Israel and Hamas in place since October 2025 that includes guarantees of increased aid.
Activists aboard past flotillas that were intercepted by Israel were deported after being detained.
Ships from the flotilla had set sail for a third time on Thursday from southern Turkey.
Israel said all 430 activists on board the flotilla's boats had been transferred to Israeli vessels and they would be allowed to meet their consular representatives after arriving in Israel.
The flotilla's organisers say participants hailed from 40 countries including Australia aboard 50 vessels.
Israel's foreign ministry said on X on Monday that it "will not allow any breach of the lawful naval blockade on Gaza".
Israeli rights group Adalah said the activists had been "detained at Ashdod port" and "taken into Israel against their will as Adalah attorneys enter for legal consultations".
The flotilla's organisers said the activists would be taken to Ketziot prison in Israel's southern Negev desert.
Without specifying how many Italian citizens were on board the flotilla, Italy's foreign ministry said they were "expected to be transferred to a facility for identification and then allowed to depart".
The foreign ministry said Italians including a member of parliament and a journalist had been on board.
Citizens of South Korea were also among those detained by Israeli naval forces, President Lee Jae-myung said on Wednesday, calling Israel's actions "way out of line".
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.
It has retained control of more than 60 per cent of Gaza since a US-backed ceasefire in October, with the militant group Hamas controlling a sliver of territory along the coast.
