There were no injuries or reports of violence. In addition to the activists, the Canadian and Irish boats were ferrying journalists and crew members from nine countries to Gaza, an area ruled by Hamas, The New York Times reported.
The Israeli navy said they first told the boats they were headed to a blockaded area and advised them to either turn around or sail to an Israeli or Egyptian port.
Israeli military spokeswoman Avital Leibovich said a short time later the boats were boarded by Israeli naval forces.
"The boarding followed numerous calls to the activists," Leibovich tweeted, adding the navy "took every precaution to ensure the safety of activists."
The boats will be steered to the Israeli port of Ashdod where the activists will be turned over to immigration authorities, the Times said.
An organizer on the Canadian boat, Ehab Lotayef, a Canadian electrical engineer of Egyptian origin, said the goal was "to say that the blockade is illegal and inhumane."
A U.N. review found Israel's blockade of Gaza preventing weapons smuggling to be legal and appropriate, the Times said.