Yonatan Shapira, an Israeli air force pilot turned peace activist, said he was shocked with a Taser gun while passively resisting arrest.
And a British journalist said he was "ambushed" and "almost strip-searched" by commandos on board the vessel.
Israel's military had said the vessel was seized peacefully on Tuesday.
It declined to comment on the activists' accounts.
Earlier this year, Israeli commandos killed nine people in clashes on board a Turkish ship trying to reach Gaza.
Israel says its blockade is designed to prevent weapons being smuggled to the militant Hamas movement which runs the territory.
Harsh treatment
Yonatan Shapira, a member of left-wing group Combatants for Peace, said he was treated "brutally" by Israeli soldiers when the ship was intercepted some 20 miles (30km) off the coast of Gaza on Tuesday.
"After they boarded, I was standing with my hands around Reuven Moskowitz, the 82-year-old holocaust survivor," he told BBC News. "We were trying to protect each other and singing: 'We shall overcome.'
"The Israeli navy captain came closer and pulled out his Taser gun and said: 'If you don't let go... it will hurt.'
"We continued to hug and he shot me twice on my right shoulder. It was painful, but not as bad as the third shot.
"He moved the life vest I had on, so he could reach closer to my heart and shot me, which made me lose control of my body. It felt like an epileptic attack or something.
"At that point I couldn't hold anything and they grabbed me brutally to the boat."
British photo-journalist Vish Vishvanath confirmed that Mr Shapira had been hit by the stun gun.
After his deportation to London, Mr Vishvanath said he had been "almost strip-searched" by Israeli special forces, who confiscated all his equipment.
"About three commandos ambushed me and took all my camera gear. They confiscated my cell phone because it had a camera on it," he told the Press Association.
He said the activists put up "a lot of resistance", but that no violence was used.
Activists freed
The Irene, dubbed the Jewish Boat for Peace, was carrying what the activists called a symbolic amount of medicine, a water purifying kit and toys.
The Israeli army diverted the boat to the port of Ashdod and said the gifts would be screened and transferred overland to Gaza.
All five Israeli activists were questioned and released without charge. Three of the four foreign nationals were deported late on Tuesday. The fourth, a German nurse, would be deported in the next few days, organisers said.
Israel and neighbouring Egypt shut down Gaza's border crossings when an Israeli soldier was captured in June 2006, and tightened the blockade further when the Islamist Hamas movement gained control of Gaza a year later.
Israel began allowing consumer goods into Gaza after its May raid on a Turkish aid ship sparked international outrage. Nine activists were killed when Israeli commandos intercepted the ship in international waters.
But it still blocks all exports from the territory, imposes a complete naval blockade, and severely restricts the movement of people.
Israel says the naval blockade is required to stop arms being smuggled to Hamas, but critics and humanitarian groups say this amounts to collective punishment of the territory's 1.5 million people.
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