A parliamentary committee says that one in five asylum seekers whose request is denied ends up in custody pending extradition, and sometimes children are detained alongside their parents.
The Control Committee of the National Council said some Swiss cantons had gone against the law by allowing the practice.
“The cantons must notice themselves that this is not permissible and it is of course regrettable that this has to be pointed out to them by the law-making bodies,” the committee's Alfred Heer told the Tagesschau news programme on SRF television.
A representative of the cantons, Roger Schneeberger, confirmed to the programme that under 15s had been kept in pre-extradition detention but “only in exceptional cases when it was in the child's interests”.
This included cases where mothers had to be taken into custody at short notice because of fears they would go underground.
The report said it was not clear how many children had been affected because no reliable figures were available.
Swiss-based international children's rights organization Terre des hommes welcomed the report, which it said was based on its own research carried out in 2016 and submitted to the federal authorities.
Terre des hommes said it had pointed out “alarming disparities between the cantons” when it came to collecting data, managing information and putting measures in place.
“All forms of detention are a traumatic experience for a child, but it is even worse in the case of very vulnerable young migrants,” the organization said.
“Like the committee, we are calling for the imprisonment of families to end, pure and simple.”
It urged Switzerland to comply with its international commitments under the 1997 UN Convention on the Rights of the Child.
The government has until the end of September to respond to the report.