Publier is breaching the country's strict laws forbidding religious symbols in public spaces, officials say.
The town, in the east, has been given three months to take down the marble statue which is on display on the shore of lake Geneva.
If it does not it will be fined for every day it is still on show.
The town's mayor Gaston Lacroix said he was going to try and find private land to keep the statue, the BBC reported.
The order to remove it has faced criticism on social media with some claiming freedom of expression is being denied by the anti-religion rules.
The law against religion in public life has long been in place in France.
