"Based on our research findings, we are extremely alarmed to hear that children have been forcibly removed and arrested from the Calais camp", said RRDP's founder Marta Welander, in a statement.
They still have their sites set on making it to the UK.
A British charity called Help Refugees said police had arrested some minors on Thursday.
Almost 800 unaccompanied minors- whose fate has been a key cause of concern on both sides of the Channel- have been moved to shipping containers converted into temporary shelters in the Jungle. He said he was joining 30 friends in a place he refused to identify that could be used as a jumping off point for clandestine, and risky, passage to England.
A CNN team at The Jungle on Thursday morning also said serious demolition was underway, with three diggers visible alongside a dozen men in hard hats and orange jumpsuits. "It is already gone but the (demolition) job will finished by Monday evening", local government prefect Fabienne Buccio told reporters as earthmovers flattened the camp, where the evacuation started on Monday.
"Yesterday RYS made further recommendations that would ensure every child still living within this very risky camp had a place to sleep".
"We have to be vigilant and make assurances that the camp is not replicated [and] stop migrants coming back", the right-wing mayor said.
Vulnerable children slept under bridges, outside warehouses and in the Jungle camp itself, which has become an increasingly volatile environment.
She had earlier vowed that the camp would shut down that night "no matter what".
French government officials have declared the operation to clear the Calais "Jungle" a success despite charities on the ground reporting that hundreds of child refugees had been left unregistered and with nowhere to go. "This kind of situation is exactly what exposes children to traffickers and smugglers, and puts them in unsafe situations without food, shelter and any support".
As part of the evacuation works, more than 200 children and adolescents with relatives in the United Kingdom were taken to that country and another large group is waiting for their cases to be approved, so the rumor that all minors will have the same fate has spread.
She said fires that engulfed wide areas of the sprawling camp after midnight and continuing Wednesday "show the camp is empty".
Dorothy Sang, a Save the Children representative at the Calais camp, said it was still not clear Thursday afternoon what those unaccompanied children who had not been registered were supposed to do. Britain took in 234 migrants with family ties in the UK.
Dismantling of the Southern part of the "jungle" of Calais. We have fulfilled our mission.