Rana Hamida, Youssef Sammour and Samuel Leason arrived at Auckland International Airport on Friday afternoon and were greeted by a crowd of supporters and loved ones.
Among the supporters were Green Party co-leader Marama Davidson and MP Ricardo Menéndez March.
Israel's foreign ministry said the claims were "complete lies", and the detainees rights were upheld.
The flotilla, a group of dozens of boats carrying 500 people - including Swedish climate campaigner Greta Thunberg - had been trying to break Israel's blockade.
Leason's father, Adi Leason, earlier told RNZ's Midday Report he was "immensely proud" of his 18-year-old son.
"We've been going to mass every Sunday for 18 years with Samuel, and he must have been listening and taking something of that formation on board. It's lovely to see a young man with a deep conscience curing so deeply about people who he will never meet and to put himself in harm's way for them."
