French officials have declared the clearance of the Calais Jungle complete with 234 children being resettled in the UK.
A total of 5,596 people have been evacuated since the operation began on Monday with many of them being taken away on buses, French ministries said.
But the announcement came as charities on the ground reported that hundreds of child refugees had been left unregistered with nowhere to go.
The prefect of Pas-de-Calais, Fabienne Buccio, said on Wednesday: "The camp is completely empty. There are no more migrants in the camp.
"Our mission has been fulfilled."
A total of 234 minors had been resettled to the UK since October 17, the French ministries of housing and the interior said.
Meanwhile, a French government minister warned it would be a "lie" to think that moving the hot-spot refugee point from Calais to Dover would end the migrant crisis
Agriculture minister Stephane Le Foll rejected calls from some leading right-wing French politicians for Paris to rip-up the Le Touquet treaty with the UK which allows British border force officers to carry out passport checks in Calais.
"We want to do our best to meet the needs of refugees. And to respect the Le Touquet agreement that Nicolas Sarkozy signed in the name of France.
"But to think that moving the hot spot to Great Britain would mean people would stop crossing the Channel would be to lie to ourselves," he told BBC Newsnight.
Mr Le Foll insisted that French authorities would not tolerate another version of the notorious Jungle refugee camp springing up.
"The right to asylum must be respected, we must also respect refugees. But we cannot accept a camp of 7,000-8,000 people in France with no response," he said.
Pascal Brice, head of the Office for Refugees and Stateless People, said everybody leaving the squalid camp had been registered at the processing centre on the edge of the site.
He spoke as firefighters fought to tackle a series of fires blamed by officials on disgruntled refugees and migrants.
But charities working with the refugees immediately contradicted the official declaration, claiming the warehouse used to register camp dwellers had been closed before many unaccompanied children living in the Jungle had been processed and transported to alternative accommodation elsewhere in France.
And migrants and refugees could be seen still walking with their belongings towards the warehouse, while other groups sat waiting in the sun in the road leading to it.
Mr Brice told reporters on Wednesday afternoon: "The operation will be over tonight because all the people who were leaving the Jungle are now welcomed in France, in good conditions in accommodation centres.
"It is a matter of satisfaction for the French administration because all those people now are in centres all around France and the Jungle is over."
A spokeswoman for the local prefecture said that the rate of demolition would be scaled up on Thursday with larger machinery moving in.
Save The Children said it was "extremely concerned" about minors who had not been registered as the site went up in flames.
Around 100 children were waiting to be processed when the warehouse was "swiftly" closed, the charity said, adding that there were hundreds with nowhere to go.
The Help Refugees charity estimated that about 300 children were turned away when the registration centre closed and many were standing under a nearby bridge not knowing what to do.
"The authorities need to get them into safety now," it tweeted.
Several large fires started tearing through caravans, tents and shelters in the centre of the camp a little before midday on Wednesday, the third day of the operation to clear it.
Four migrants have been arrested in connection with the fires, said Patrick Visser-Bourdon, the Calais police commissioner in charge of the operation, dismissing suggestions British activists were responsible.
The sound of exploding gas canisters could be heard as the flames ripped through what had recently been makeshift homes.
Firefighters used hoses to tackle the flames gutting the Peace restaurant, which days ago was serving tea to residents.
A bus for women and children and a makeshift youth centre were also burned down, according to Help Refugees.
As the fires spread, police ushered people out of the camp, many of whom held fabric to their mouths and noses to protect against the thick black smoke.