In a post on X just before 10.30am (5.30pm AEST), the Foreign Ministry shared a photo of Thunberg on a plane.

“Greta Thunberg just departed Israel on a flight to Sweden (via France),” the post said.

Adalah, a legal rights group in Israel that represents Thunberg, has stated that she, along with two other activists and a journalist, has agreed to deportation and will depart from Israel.

Other activists refused deportation, were being held in detention and their case was set to be heard by Israeli authorities.

Thunberg was one of 12 passengers on board the Madleen, a boat carrying aid destined for people in war-torn Gaza.

The group of activists declared that their mission was to protest against the ongoing conflict and humanitarian situation in Gaza. Meanwhile, Israel maintains that these ships are in violation of its naval blockade on Gaza.

The foreign ministry said they underwent medical examinations earlier in the day after docking in the Israeli port of Ashdod.

On arrival to Ashdod, the activists were taken to a room to be shown a screening of the “horror film documenting the October 7 massacre” carried out by Hamas, according to Israeli Defence Minister Israel Katz.

“When they saw what it was about, they refused to continue watching,” Katz said.

He accused Thunberg and the rest of the ship’s crew of ignoring Hamas atrocities by “closing their eyes to the truth.”

The Freedom Flotilla Coalition (FFC) said the Israeli military had “attacked” and “unlawfully boarded” the Madleen, which was attempting to deliver aid to Gaza – where more than 600 days of war, and an 11-week Israeli blockade of all aid, has pushed the enclave’s 2.1 million people deeper into a hunger crisis.

The ministry also previously posted a video showing members of the Madleen crew sitting side by side wearing orange life jackets while a solider offered them bottled water and plastic-wrapped sandwiches. Thunberg can be seen sitting near the front of the group.

The FFC had earlier said the ship had come “under assault in international waters” in a Telegram post.

“Quadcopters are surrounding the ship, spraying it with a white paint-like substance. Communications are jammed, and disturbing sounds are being played over the radio,” the FFC said.

A video posted by Israel’s foreign ministry appeared to show a Navy staffer sending a radio message to the vessel saying the “maritime zone off the coast of Gaza was closed”.

In a video livestreamed from the boat, activist Yasemin Acar showed a white substance on the deck, saying it had been dropped on the vessel. Acar was later heard saying it was affecting her eyes.

The FFC group also posted a video on Telegram, showing members of the crew sitting inside the boat with their hands in the air.

After losing communication with the vessel, the FFC began posting pre-recorded video messages from Thunberg and others onboard. “If you see this video, we have been intercepted and kidnapped in international waters by the Israeli occupational forces, or forces that support Israel,” Thunberg said in her video.

In a statement, the FFC said Israel had acted with “total impunity” and that the vessel’s cargo, which included baby formula, food and medical supplies was “confiscated”. Israel said it would transfer the goods to Gaza through humanitarian channels.

“Israel has no legal authority to detain international volunteers aboard the Madleen,” said Huwaida Arraf, human rights lawyer and Freedom Flotilla organiser.

“This seizure blatantly violates international law and defies the (International Court of Justice’s) binding orders requiring unimpeded humanitarian access to Gaza.”

Amnesty International also condemned the detention of the activists.

In a statement to CNN, Israel said that it “is preventing the entry of all vessels into the Gaza Strip, in accordance with international law”.

Israel had repeatedly vowed to stop the aid boat from reaching Gaza, and described the ship as a “selfie yacht” carrying “celebrities”.

Israel’s Foreign Ministry said the group “attempted to stage a media provocation whose sole purpose was to gain publicity”.

“There are ways to deliver aid to the Gaza Strip – they do not involve Instagram selfies,” it added.

The French Foreign Ministry said on Monday that there were six French nationals on board the Madleen, and that it is in contact with Israeli authorities to bring them back. The French government had previously warned the activists against their plan.

Hamas demanded the immediate release of the activists and condemned their detention in a statement, calling the interception “a flagrant violation of international law, and an attack on civilian volunteers acting out of humanitarian motives”.

Israel imposed a full humanitarian blockade of Gaza on March 2, cutting off food, medical supplies, and other aid to the more than 2 million Palestinians who live in the territory for 11 weeks.

Faced with growing international pressure, Israel began allowing a trickle of aid in late May. But humanitarian organisations say it is only a fraction of the aid that entered the enclave before the war, and have warned of a worsening humanitarian crisis and the growing risk of widespread famine. A UN-backed report warned in late April that one in five people were facing starvation.