Dozens of children have reportedly been forced to sleep on the roadside of the Calais Jungle, despite French officials declaring the clearance complete.
Images showed youngsters lying on blankets in the dirt, after allegedly being turned away from the part of the camp where they had been staying for safety.
On Thursday morning, volunteers said "at least 100 children" were queueing for a registration process which had been ended on Wednesday.
A total of 5,596 people have been evacuated since the operation began on Monday, with many being taken away on buses, French ministries said. But charities claimed many young refugees were left without safe haven after fires ravaged the makeshift site, cutting short the registration process for camp dwellers.
Save The Children said it was a "recipe for disaster" for the children left outside, many of whom fled or were exposed to the risk of people smugglers.
Spokeswoman Dorothy Sang, who is in the camp, said: "What happened yesterday put children in a serious amount of danger. Yesterday afternoon we saw fires rage through the camp and as children ran out, they ran out to find the registration process had been closed for a couple of hours, so there was nowhere for them to register to go and stay safe.
"Not only this but the containers were full, so you had this situation where children were running away from fire, couldn't register and the containers were full - so there was literally nowhere for children to go."
She said the streets that lead to the camp were lined with at least 60 youngsters, but other estimates had put the numbers a lot higher. A handful of them were allowed to stay in a warehouse, but some were turned away, she added.
Charity Help Refugees added in a post on Thursday: "This morning, at least 100 children were waiting in the minors' line to be processed at the registration centre. The centre was closed, and no officials present."
The prefect of the Pas-de-Calais region, Fabienne Buccio, said on Wednesday: "The camp is completely empty. There are no more migrants in the camp. Our mission has been fulfilled."
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.
Despite this, campaigners said on Thursday that official estimates of the amount of people processed were lower than the total said to live in the camp, fuelling concerns that thousands could be left in the area.