Tunisia said on Wednesday the "assault" on a ship at Sidi Bou Said port was "orchestrated," after the Global Sumud Flotilla, preparing to deliver aid to Gaza, reported one of its boats was attacked by a drone in the second such strike in two days.
GSF is set to sail for Gaza in an effort to break Israel's naval blockade, following two nights of drone attacks on key vessels in the convoy which organisers described as deliberate attempts by Israel to disrupt the mission.
The Israeli military did not respond to a request for comment.
There were no injuries, and civil protection authorities brought a fire on the boat under control on Wednesday night.
The Tunisian interior Ministry, which did not accuse any party or country, said in a statement that it was conducting investigations into the drone attack.
The United Nations' Special Rapporteur on the occupied Palestinian territories, Francesca Albanese, told Reuters on Tuesday "it is an attack against Tunisian sovereignty".
Earlier on Wednesday, thousands of Tunisians gathered on the picturesque beach of Sidi Bou Said to support pro-Palestinian activists on the boats, one of the biggest flotillas yet to set sail for Gaza.
The flotilla, which includes hundreds of activists and dozens of boats, is supported by delegations from 44 countries, including Swedish activist Greta Thunberg and Portuguese left-wing politician Mariana Mortagua.
Israel has maintained a siege on the coastal enclave since 2007, which has been described by rights groups as turning the Palestinian territory into the "world's largest open-air prison".
The blockade has remained in place and intensified through the current war, which is being increasingly recognised around the world as a genocide.
Israel's military assault on Gaza has killed over 64,000 Palestinians, while a crippling famine induced by Israel's blockade has killed hundreds.
Israel sealed off Gaza by land in early March, letting in no supplies for three months, leading to the widespread shortage of food.