The Israeli Foreign Ministry said on X that the activists were "currently undergoing medical examinations to ensure they are in good health".
It also published a photo of Thunberg after she disembarked.
The Madleen, from the Freedom Flotilla Coalition (FFC), set sail from Sicily one week ago carrying aid for Palestinians and hoping to add pressure on Israel to end the war in the Gaza Strip.
However, they were intercepted by Israeli forces early on Monday after an order from Defence Minister Israel Katz.
The activists were expected to be handed over to the police and prison authorities to be "medically examined and registered".
They were then to be offered the opportunity to watch a video of the atrocities committed by the Palestinian militant group Hamas in the October 7, 2023 attacks on Israel, before being returned to their home countries via the Ben Gurion International Airport.
In a statement earlier on Monday, the FFC said the Madleen had "been attacked/forcibly intercepted by the Israeli military" in international waters.
"The ship was unlawfully boarded, its unarmed civilian crew abducted, and its life-saving cargo - including baby formula, food and medical supplies - confiscated," the FFC said in a statement.
FFC organiser Huwaida Arraf said Israel had no legal authority to detain those aboard the ship.
"These volunteers are not subject to Israeli jurisdiction and cannot be criminalised for delivering aid or challenging an illegal blockade - their detention is arbitrary, unlawful and must end immediately," Arraf said.
"We are undeterred. We will sail again. We will not stop until the siege ends and Palestine is free," the FFC said.
The activists argue that Israel must guarantee unhindered humanitarian access to the coastal strip.
The Israeli Foreign Ministry, however, stated that the zone off the Gaza Strip is closed to unauthorised vessels under the naval blockade in place since 2007.
A spokesperson for the Israeli Foreign Ministry labelled the international activists' action a "provocation" and a "gimmick" while the ministry has labelled the Madleen a "selfie yacht".
Progressive Israeli activists protested in Ashdod against the military's deployment, holding up signs calling for the government to "end the blockade, the hunger, the genocide".
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