The British-flagged yacht, Madleen, operated by the pro-Palestinian Freedom Flotilla Coalition, was aiming to deliver a symbolic amount of aid to Gaza later on Monday and raise international awareness of the humanitarian crisis there.
"If you see this video, we have been intercepted and kidnapped in international waters by Israeli occupational forces or forces that support Israel," Thunberg, 22, said in a video released by the coalition, filmed before the vessel was captured.
"I urge all my friends, family and comrades to put pressure on the Swedish government to release me and the others as soon as possible."
The Israeli Foreign Ministry confirmed the vessel was under Israeli control.
Israel has called Thunberg an "anti-Semite" and dismissed the aid ship as a stunt.
"The 'selfie yacht' of the 'celebrities' is safely making its way to the shores of Israel. The passengers are expected to return to their home countries," the ministry wrote on X.
All passengers were safe and unharmed, the ministry later said.
"They were provided with sandwiches and water. The show is over."
Rima Hassan, a French member of the European parliament who was also on board, posted on X that the crew had been "arrested by the Israeli army in international waters around 2am".
The yacht was carrying a small shipment of humanitarian aid, including rice and baby formula.
The Foreign Ministry said it would be taken to Gaza.
"The tiny amount of aid that was on the yacht and not consumed by the 'celebrities' will be transferred to Gaza through real humanitarian channels," it wrote.
The Swedish foreign ministry said it was in contact with Israeli authorities.
"Should the need for consular support arise, the Embassy and the Ministry of Foreign Affairs will assess how we can best help the Swedish citizen/Greta Thunberg resolve her situation," a Swedish Foreign Ministry spokesperson said in a statement.
French President Emmanuel Macron's office said the president had asked Israeli authorities to release the French nationals on board as soon as possible.
Israeli Defence Minister Israel Katz ordered the military on Sunday to prevent the Madleen from reaching Gaza, calling the mission a propaganda effort in support of Hamas.
Katz said he had instructed that upon the boat's arrival at Ashdod port, the activists would be shown videos of atrocities committed during the October 7, 2023, Hamas-led attack on southern Israel, which triggered the Gaza war.
Hamas condemned the seizure of the boat as "state terrorism" and said it saluted its activists.
Israel imposed a naval blockade on the coastal enclave after Hamas took control of Gaza in 2007.
The blockade has remained in place through multiple conflicts, including the current war, which began when Hamas-led militants rampaged through southern Israel on October 7, 2023, killing more than 1200 people and taking 251 hostages, by Israeli tallies.
Israel's retaliatory offensive against Hamas has since killed more than 54,000 Palestinians, according to health officials in Hamas-run Gaza and left its more than two million population largely displaced and at risk of famine, according to the United Nations.
The UN special rapporteur on human rights in the Palestinian territories, Francesca Albanese, has supported the Madleen operation and on Sunday, urged other boats to challenge the Gaza blockade.
"Madleen's journey may have ended, but the mission isn't over," she wrote on X.
