Unite Union boss Mike Treen has allegedly been "repeatedly tasered" by Israeli Defense Forces (IDF), receiving injuries to his face and head.
Mr Treen is currently detained in Givon Prison and is recovering from his injuries, according to Unite Union.
He was taking part in an aid convoy to Gaza on the ship Al Awda when it was intercepted by the IDF on Monday (local time).
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Mr Treen told Unite Union his fellow flotilla members were tasered in the head. A 69-year-old woman received a head injury and a senior Canadian passenger received a foot injury and had to be treated in hospital.
Local civil rights lawyers have met with the detained people and learned all their belongings, including their passports, have been seized and not returned, despite promises they would if they co-operated.
The union says Mr Treen was there on a peaceful mission and is is calling on the Government to intervene.
"Mike was taking part in a peaceful mission to deliver aid to Gaza and was in international waters when attacked and detained. We understand he has been taken, kidnapped in reality, to the southern Israeli port of Ashod," said National Secretary Gerard Hehir on The AM Show.
"We expect the New Zealand Government to strongly protest and demand his immediate release, along with his fellow campaigners and the Al Awda so they can deliver the much needed medical aid to the port of Gaza."
Mr Treen has been detained in similar circumstances to Green Party co-leader Marama Davidson, who took part in a flotilla to Israel in 2016.
She has called for the Government to intervene in Mr Treen's detainment.
"I will always be grateful that I had the opportunity to be part of the women's peace boat to Gaza in 2016 and I hope Mike fares well," she wrote on Facebook.
"He is a staunch advocate for peace through justice and will have an important story to tell the world."
The Embassy of Israel in New Zealand said in a statement that the flotilla is a violation of international law and is "a cynical publicity stunt designed to divert the attention from the fact that Hamas, with its brutal ruling of Gaza since 2007, invested in terror instead of the welfare of its people."