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Captain Pete Bethune, of Earthrace Conservation, was attacked by the pair in the port city of Santander on Tuesday morning.
Bethune said one of the men lunged at him with a knife while a second man came from behind. A fight ensued and Bethune received a knife wound to the chest.
The pair left the scene with Bethune's cellphone and Bethune hitched a motorcycle ride back to his motel in Macapa.
He patched his wounds up with dressings and was rushed to Macapa Hospital shortly after. In a Facebook post a spokeswoman from Earthrace Conservation said it wasn't yet clear how bad Bethune's injuries were.
Macapa police are investigating the circumstances around Bethune's injuries.
The Kiwi called the incident a "frightening ordeal".
"I honestly thought I was going to die today."
Bethune had recently left the Amazon, where he had been working with the Earthrace team for several months on various conservation issues.
It wasn't believed the attack was related to the work of Earthrace Conservation.
Back in 2010 the Auckland-based activist spent four months in a Tokyo jail after assaulting a whaler by hurling a rancid butter stink bomb during a high-seas confrontation.
He pleaded guilty to obstructing commercial activities and charges stemming from climbing aboard the Japanese ship - trespass, vandalism and carrying a knife, with which he cut the ship's security netting.
But he denied the assault, which prosecutors said left a 24-year-old whaler with chemical splash burns to his face following the February 11 confrontation in which Sea Shepherd activists hurled the stink bombs.