The decision was made on Thursday when Judge Valerie Quemener upheld a proposed government plan to demolish the site.
The decision came after numerous charity groups as well as an estimated 250 residents made an appeal to suspend the evacuation.
"The order is applicable, except for common social areas," the spokesman for the Pas-de-Calais prefect's office told Reuters. "So it won't be applicable to places such as schools, a theatre and a legal office."
At least 1,000 refugees currently residing in the area are to be moved from the northern French port, with authorities suggesting force will be used "if necessary".
However, authorities have ensured the evacuation procedure will be gradual.
"Carrying out a brutal eviction in the south part of Calais with bulldozers was never envisaged," said Bernard Cazeneuve, French Interior Minister.
London2Calais, a British voluntary organisation, responded saying it "considers that the proposed evictions, which go against all the demands of humanitarian organisations, are a cruel and repressive assault on defenceless people".
"It should be resisted by all means necessary," the group's spokesperson told The New Arab.
Alternative accommodation is available for migrants in a container park nearby, but the makeshift camp does not have key facilities - including toilets or showers.