Volunteers from Help Refugees said that dozens of children stranded in the camp spent the night sleeping on the floor of the church and school. The volunteers brought the group blankets and food and stood guard over them through the night.
Home Secretary Amber Rudd has called on French authorities to "properly protect" children, after reports surfaced that people had been forced to sleep rough around what remains of the camp.
An operation to clear the camp began on Monday. A reported 5,596 people have been evacuated from the site so far. Help Refugees reported this morning that all residents must be registered with authorities by 2.00pm on Friday. Anyone without a wristband will face arrest.
The operation has been criticized for exposing dozens of unaccompanied children to "serious amounts of danger" by charity Save the Children.
A Home Office spokesman said: "The Home Secretary has today spoken again with her French counterpart Bernard Cazeneuve to stress the need for children who remain in Calais to be properly protected.
"Any child either eligible or not in the secure area of the camp should be cared for and safeguarded by the French authorities. We understand specialist facilities have been made available elsewhere in France to ensure this happens," the spokesman added.
Campaigners said on Thursday that official estimates of the amount of people processed at the site were lower than the total said to live in the camp, increasing concerns that thousands could be left in the area.
A total of 234 minors have been resettled to the UK since October 17.