Prime Minister Benjamin Netanyahu praised Israeli naval forces on Thursday for intercepting a Gaza-bound aid flotilla, as authorities prepared to deport hundreds of pro-Palestinian activists aboard the vessels.

The Global Sumud Flotilla of around 45 vessels began its voyage last month, with politicians and activists, including Swedish climate campaigner Greta Thunberg heading to Gaza, where the United Nations says famine has set in.

The Israeli navy has intercepted vessel after vessel at sea since Wednesday, after warning the activists against entering waters it says fall under its blockade, with Thunberg's boat among those stopped from going further.

"I commend the soldiers and commanders of the navy who carried out their mission on Yom Kippur in the most professional and efficient manner," Netanyahu said in a statement.

"Their important action prevented dozens of vessels from entering the war zone and repelled a campaign of delegitimisation against Israel."

An Israeli official said more than 400 activists aboard 41 vessels were detained. Israel said the activists would be deported to Europe.

Rights group Amnesty International criticised Israel for blocking the flotilla, saying it was an "act of intimidation intended to punish and silence critics of Israel's genocide and its unlawful blockade on Gaza."

Hamas, whose October 7, 2023 attack on Israel sparked the war in Gaza, condemned the interception of the flotilla as a "crime of piracy and maritime terrorism."

With the war in Gaza dragging on, solidarity with the Palestinians has grown globally, with activists and, increasingly, governments, condemning Israel for its conduct.

Spain and Italy, which both sent naval escorts to protect their citizens on board the flotilla, had urged the activists to halt before entering Israel's declared exclusion zone off Gaza, saying they would not be allowed to pass that mark.

The boats, with dozens of activists from around the world on board, initially set sail from several European ports.

After a 10-day stop in Tunisia, where organisers reported two drone attacks, the flotilla resumed its journey on September 15. (AFP)