Several hundred migrants remain inside the “Jungle” camp in Calais, say BBC reporters at the scene, despite French officials claiming the camp is now empty.
About 100 unaccompanied minors were left with nowhere to sleep overnight, aid workers say.
They are said to be becoming increasingly desperate.
Nearly 5,600 people have been moved to reception centres since Monday, the government said (in French).
This includes about 1,500 unaccompanied minors being housed in an on-site container camp, which activists say is now full.
Demolition crews continued to clear tents and shelters from the area on Wednesday amid smouldering fires reportedly set by departing migrants.
Fabienne Buccio, the prefect of Pas-de-Calais, said it was “mission accomplished” for the operation.
The camp has become a key symbol of Europe’s migration crisis, with its residents desperate to reach the UK.
Caroline Gregory of Calais Action, a British charity, said about 100 unaccompanied children had been left in the camp overnight.
“We were begging the French authorities to actually do something about the refugee children and nothing was done,” she told the BBC on Thursday.
Volunteers found shelter for the children in a warehouse where many of the migrants were being processed, as well as a makeshift school inside the camp.
‘Our mission is over’
The UK Home Office said French authorities were responsible for “all children in Calais during the clearance operation – including those being assessed for possible transfer to the UK”.
It was responding to a letter from Baroness Sheehan to Home Secretary Amber Rudd expressing her “extreme anger” after having seen some 100 mostly teenage boys being denied access to a processing centre on Tuesday night.
Fires burned at the camp during the clearance work throughout the week.
Ms Buccio told local media it was “a tradition among the migrant population to destroy their homes before leaving”.
One man was reported to have been injured when a gas canister exploded in the flames.
More than 1,200 police officers have been deployed for the clearance operation at the camp, which is unpopular locally and has required a large security presence to prevent migrants reaching the UK on lorries or trains heading across the Channel.
Since the start of the week, French authorities have been bussing thousands of people to shelters and centres where they will be able to seek asylum.
The demolition operation started on Tuesday afternoon
The operation has gone faster than expected and on Wednesday afternoon Ms Buccio said: “It’s the end of the Jungle, our mission is over. There are no more migrants in the camp.”
A total of 5,596 people, including children, have been transported from the Jungle for resettlement, the French government says. This includes 234 minors brought to the UK since last week.
The camp had an estimated 6,000-8,000 residents. Authorities fear they will return to set up camp again once the clearance operation is over.