The blazes spread just hours after workers protected by police moved in Tuesday to clear the squalid camp that has been home to an estimated 6,000-8,000 migrants, many with hopes of reaching Britain.
"Our tents were burning. Someone set fire to them, though I don't know who," said Siddiq, a 16-year-old boy, who was forced by the flames to sleep under a bridge at the camp's entrance.
"I have seen many fires before but not like this."
A Syrian man was taken to hospital with injuries to his ear drums after a gas canister exploded in the flames, which ravaged one of the main thoroughfares in the camp.
A local official downplayed the blazes, telling reporters: "It's a tradition among communities who set fire to their homes before leaving."
On Tuesday workers in hard hats and orange overalls used power saws to reduce shacks to piles of wood and plastic that were removed by diggers.
Mattresses, blankets, clothes, pots and suitcases left behind by migrants were also carted away.
Located next to the port of Calais, the Jungle has for years been a launchpad for migrants attempting to make it to Britain by sneaking onto lorries or jumping onto trains heading across the Channel.
As part of the camp's clearance, 3,242 adults have been transferred to centres around France since Monday and 772 unaccompanied minors have been moved to shipping containers converted into temporary shelters in the Jungle, the interior ministry said.
The numbers represent around half the camp's estimated population before the operation began, according to official figures.
The authorities have said those who agree to be moved can seek asylum in France. Those who refuse risk deportation.