The Israel Navy and Shin Bet intelligence agency have disclosed that the boat seized last month was carrying materials for making weapons.
The boat was intercepted on 19 January and arrested three suspected Palestinian smugglers.
The Jerusalem Post cited security officials as saying that the boat, which was travelling from Sinai to the Gaza Strip, has been carrying fibreglass resin, a material used for the production of rockets.
The three suspects reportedly admitted the Shin Bet during questioning that the liquid fibreglass was intended to assist the armed wing of the Islamist Hamas movement, the Ezzedine al-Qassam Brigades, by providing it with raw material for the development of rockets and mortar shells in Gaza.
Israel Defense Force spokesman lieutenant colonel Peter Lerner told The Jewish Press: "The IDF is determined to prevent unlawful attempts to ship weapons and raw materials that may jeopardise the well-being of Israelis.
"This shipment highlights that when Hamas chose to smuggle materials for rockets and mortars, it chose not to invest in the rehabilitation for the people of Gaza."
Information regarding the sea-based smuggling between Gaza and Sinai has also been revealed by the three men, during the questioning.
The Times of Israel cited the Shin Bet as saying: "Recently, Hamas has invested much in exploiting naval smuggling routes, partly due to Egypt’s efforts to prevent smuggling tunnels that linked Sinai and Gaza."