The hunter mistook the jackal for a fox but once he realized his error, he contacted wildlife officials, Graubünden's hunting and fishing department said on Wednesday.
He shot the male golden jackal in the Surselva district in the western part of the canton a few days ago, the department said in a news release.
The accident occurred shortly after a photograph of a golden jackal was taken by a camera trap with a sensor in the same district on December 27th, the release said.
It is not clear whether the animal killed as the one photographed, the hunting department said.
Several photos of a golden jackal were taken in 2011-2012 with a camera trap but there have been no human encounters.
The animal is a protected species with the same status in Switzerland as larger carnivores, such as the lynx, bear and wolf, and it is against the law to hunt it.
A medium-sized member of the Canidae family, the golden jackal weighs from eight to 15 kilograms and is bigger than a fox but smaller than a wolf.
The animal killed by the hunter weighed 11.2 kilograms, the Graubünden hunting department said.
With longer legs than a fox but a shorter tail, the golden jackal eats small to medium sized vertebrates, insects and fruits but can also tear into sheep and goats, the department said.
It said the presence of this species of jackal in Switzerland appears to confirm its spread from southeastern Europe to Central Europe.
The jackal's presence has been detected in Austria and northeast Italy since 2007.