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Israel's military says soldiers boarded the Irish-owned Rachel Corrie from the sea and did not meet any resistance.
It says the ship is now being taken to the Israeli port of Ashdod. There has been no word from those on board.
The incident comes five days after nine people were killed in clashes when troops boarded a Turkish aid ship, prompting international criticism.
Israel says it will question those on board at the port and transfer the aid to the Gaza Strip by land after checking the cargo for banned items.
There are five Irish and six Malaysian pro-Palestinian activists, plus several crew, on the boat.
The Rachel Corrie is named after a US college student who was crushed to death by an Israeli army bulldozer as she protested over house demolitions in Gaza in 2003.
Israel has blockaded Gaza since 2007, when the Islamist Hamas movement seized control of the territory.
'Full compliance'The 1,200 tonne cargo ship was boarded about 16 nautical miles (30km) off the Israeli coast.
An Israeli military spokeswoman said there "was full compliance from the crew and passengers on board".
The ship had previously ignored repeated requests to change course, the Israeli military said.
The sea-borne mission has been organised by the Cyprus-based Free Gaza Movement, a coalition of pro-Palestinian groups and human rights organisations.
A spokeswoman for the Free Gaza Movement, Greta Berlin, said Israel's takeover of the ship was "another outrage to add to the nine murdered", the Associated Press news agency reported.
Israeli government spokesman Mark Regev accused the group of hypocrisy, saying "While they appear to use the language of human rights in, their propaganda, it appears they have embraced the [Hamas] regime that has no respect for human rights whatsoever," AP said.
The Rachel Corrie is carrying hundreds of tonnes of aid, including wheelchairs, medical supplies and cement. Construction materials are banned from entering Gaza by Israel, which says they could be used for military purposes by Hamas.
Israel came under fierce criticism after its troops shot dead nine people during a violent confrontation with those on board the Turkish Mavi Marmara in the early hours of Monday
Israel says its commandos were attacked with weapons, including knives, and opened fire in self-defence. Activists on the ship say troops shot at them without provocation.