A judge upheld a government order on Thursday to evict migrants living in the southern part of the camp although a few makeshift buildings of social importance such as a school and a theater will be left untouched.
Interior Minister Bernard Cazeneuve said authorities would work with humanitarian organizations to relocate migrants to a nearby park of converted shipping containers or other reception centers around the country.
Thousands of migrants fleeing war and poverty, from Afghanistan to Syria, have converged on the northern port over the past year.
Most attempt to climb illegally onto trains using the Channel Tunnel or lorries heading to Britain where they hope to settle.
Their presence has led to tension with some of the local population and permanent police deployment.
Regional prefect Fabienne Buccio has said the evacuation would be gradual, with increased patrols of immigration officers meeting with refugees in the coming days.
Charity groups believe around 3,400 people including women and children live in the earmarked area, more than triple the official estimate.
The interior ministry says 200 beds are still available in the container park opened earlier this year with a capacity of 1,500.