The upcoming voyage follows two previous flotilla attempts that captured international attention.
The Madleen was intercepted by Israeli naval forces in international waters as it approached the blockade.
Thunberg, who has been vocal on the Israel-Palestine conflict after rising to prominence due to her involvement in climate activism, pictured receiving a challah sandwich from soldiers as the crew were diverted to Ashdod.
Israeli officials said the vessel contained a symbolic quantity of aid, some of which had been eaten by the crew, which would be directed to Gaza via the proper channels.
The Foreign Ministry called the vessel a “selfie yacht” and said passengers would be shown October 7 footage “so they understand who they were trying to help”.
Thunberg later claimed that the crew had been “kidnapped”, saying: “I was very clear in my testimony that we were kidnapped on international water and brought against our will into Israel.”
She signed a self-deportation order and was sent home to her native Sweden, reportedly to the outrage of her comrades who had refused to sign.
The first flotilla voyage, meanwhile, was cut short when that vessel came under aerial assault off the coast of Malta.
The crew blamed Israel for the alleged drone attack, but refused to allow Maltese authorities on board to verify the damage.
All 12 passengers were brought safely ashore while the ship remained outside Malta’s territorial waters.