Originally, Northern Territory Police said the man's injuries were not considered life-threatening and he was undergoing emergency surgery.
However, a spokesperson for Northern Territory Heath said the man's condition had worsened and he was described as "critical”.
It's believed the man was employed as an egg harvesting operator
The collection of eggs was made legal in 2018 under a commercial wildlife harvesting licence subject to strict requirements.
Collectors can earn $30 AUD an egg, earning $1,800 from a single nest of up to 60 eggs.
The eggs are transported to crocodile farms where they are raised and then killed to make luxury crocodile leather products.
NT WorkSafe is investigating the incident.