Project Chariot was criticized for the potential environmental impact it would have on the local wildlife. University of Alaska researchers said that the Arctic Tundra's food chain faced a particular risk, and caribou had already been affected by atmospheric strontium-90 due to its absorption by lichens. The risk to wildlife would naturally impact local native populations as well, as they subsisted on caribou and other animals.
The project was also criticized by business leaders, who were skeptical about how useful a deepwater arctic harbor would really be, considering that the water would spend approximately nine months out of the year frozen. Additionally, the existence of valuable natural resources in the area was mostly speculation at the time. Once oil was eventually discovered, the Trans-Alaska Pipeline was built to handle its transportation rather than relying on boats.
In 1962, the Atomic Energy Commission announced that Project Chariot would be "held in abeyance," and work on it was shelved indefinitely.