Defence Minister Israel Katz said that Israel would not allow anyone to break its naval blockade of the Palestinian territory, which he said was aimed at preventing Hamas from importing arms.
"To the anti-Semitic Greta and her fellow Hamas propagandists - I will say this clearly: you should turn back, because you will not make it to Gaza," he said in a statement.
Thunberg, a climate campaigner, is among 12 activists aboard the Madleen, which is operated by the Freedom Flotilla Coalition.
The vessel departed Sicily last Sunday on a mission that aims to break the sea blockade of the Gaza Strip and deliver humanitarian aid, while raising awareness over the growing humanitarian crisis 20 months into the Israel-Hamas war.
The activists had said they planned to reach the Gaza Strip's territorial waters as early as Sunday.
Thiago �vila, a Brazilian activist on board the boat, posted a video on social media on Sunday afternoon saying someone appeared to be jamming their tracking and communication devices about 160 nautical miles from the strip.
Rima Hassan, a French member of the European Parliament who is of Palestinian descent, is among the others onboard.
She has been barred from entering Israel because of her opposition to Israeli policies toward the Palestinians.
After a two and a half month total blockade aimed at pressuring Hamas, Israel started allowing some basic aid into the Gaza Strip last month, but humanitarian workers have warned of famine unless the blockade is lifted and Israeli forces ends their military offensive.
An attempt last month by Freedom Flotilla to reach the Gaza Strip by sea failed after another of the group's vessels was attacked by two drones while sailing in international waters off Malta.
The group blamed Israel for the attack, which damaged the front section of the ship.
Israel and Egypt have imposed varying degrees of blockade on the Gaza Strip since Hamas seized power from rival Palestinian forces in 2007.
Critics of the blockade say it amounts to collective punishment of the territory's roughly two million Palestinians.
Israel sealed the Gaza Strip off from all aid in the early days of the war ignited by the Hamas-led attack on southern Israel on October 7, 2023 but later relented under US pressure.
In early March, shortly before Israel ended a ceasefire with Hamas, the country again blocked all imports including food, fuel and medicine.
Hamas-led militants killed about 1200 people, mostly civilians, in the October 7 attack and abducted 251 hostages, more than half of whom have since been released in ceasefire agreements or other deals.
Hamas is still holding 55 hostages, more than half of them believed to be dead.
Israel's military campaign has killed more than 54,000 Palestinians, according to the Gaza Health Ministry, which has said women and children make up most of the dead.
It does not say whether those killed are civilians or combatants.
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