The Finnish-flagged Estelle left Naples on 7 October with some 20 people of eight different nationalities aboard.
Israel imposed the blockade after the Islamist group Hamas seized control of the coastal sliver in 2007.
An IDF spokesperson confirmed the navy had boarded the ship and that no-one had been injured, but provided few further details.
The boat was boarded 30 nautical miles off the coast of Gaza, activists said, and was then being taken to the Israeli port of Ashdod.
The Estelle, which is reportedly carrying a cargo including cement and medical supplies, is the latest vessel to try and break the Gaza blockade.
It comes two years after nine Turkish activists were killed in an Israeli navy raid on the Mavi Marmara, one of a flotilla of ships attempting to break the blockade.
Palestinians say Israel’s blockade of the Gaza Strip amounts to collective punishment to residents of the densely populated strip of land along the Mediterranean coast.
Israel says the blockade aims to stop the supply of arms or other items for military use, and to put pressure on the Hamas administration.
International pressure following the deadly 2010 interception led Israel to ease its blockade, allowing more food products into the strip.
The movement of people and construction materials – such as cement and steel cables – is still heavily restricted.
The importing of all weapons and military materials is banned, along with dual-use materials such as fertilizers and certain chemicals.
Fishermen may only operate in a strip of water up to three nautical miles from the shore.
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