The Act, which became law last week, gives the government powers to demand that unaccompanied asylum seekers under 18 report daily or weekly to an immigration officer, as well as an option to impose curfews.
The Home Office says these powers will help stop young asylum seekers absconding. But refugee and children's charities warned it will disrupt their school day, cause unnecessary fear, and compromise their human rights and personal safety.
Lisa Nandy, policy adviser at The Children's Society, said: "This is totally unnecessary. These children are in the care of the local authority, so if they absconded it would be flagged up quickly anyway.
"This appears to contradict the Every Child Matters agenda and gives the impression that the government seems to have forgotten that these are vulnerable children."
Sheree Kane, principal officer for children in public care at the National Children's Bureau (NCB), is particularly concerned about the effect of the reporting process on children, describing it as an intimidating experience.
She said reporting is likely to involve lengthy trips to regional offices, which will almost certainly cause children to miss lessons and even take an entire day off school.
Another concern for the NCB is the resource implications, with a foster carer or social worker accompanying the child on the immigration office visit.
A Refugee Council spokesman said the only other group the power is likely to apply to is foreign national prisoners. "To lump children in the same group as prisoners just doesn't make sense. These children have already been granted leave to remain in the country and to put this extra burden on them is inconsistent with all other human rights standards." he said.
A Home Office spokeswoman said work on a code of practice for the Border and Immigration Agency has just begun. Public consultation will follow before the code is finalised in 2008.
- Additional reporting by Tristan Donovan