The federal office of highways ruled that the signs, approved by the canton, did not conform to national standards.
They were erected earlier this year on the Route de Verbois, in the western part of Geneva, in a bid to reduce accidents involving the wild rodent.
The Contact Castor association had sought approval for the signs, featuring a red triangle and the image of a beaver, on a section of the road near a Rhône River dam used as a corridor by the animals.
The group is upset by the federal government’s decision, which it regards as overly bureaucratic.
“Accidents on the road cause many beaver deaths,” Olivier Bodmer, founder of Contact Castor, told the Tribune de Genève newspaper.
“It’s also a question of safety for motorists,” Bodmer said.
Beavers can weigh close to 30 kilograms and a collision with one can cause major damage to a vehicle, he indicated.
The signs — the first of their kind in Switzerland — were nonetheless removed earlier this month at the insistence of federal authorities.
The only wildlife warning road sign permitted by the highways office is one with a red triangle surrounding an image of a deer.
This is regardless of whether the animals in the area of the sign are other species, such as foxes, badgers, wild boars or hedgehogs.
Gottlieb Dändliker, cantonal wildlife inspector, believes the signs made sense.
“It is genetically important that families of beavers living upstream and downstream of the dam can mix,” he told the Tribune de Genève.
After becoming extinct in Switzerland, beavers were reintroduced to the country in the late 1950s.
They can now be found in several regions, apart from Geneva.