"After a particularly alarming period the young patients' health has improved markedly and there is no longer any immediate threat to their lives," Lausanne university hospital said in a statement.
No date has been set for their repatriation, but they are expected to go home soon, it said.
The coach was returning from a ski trip with 46 children, four teachers and two drivers on board when it smashed into the wall of a Swiss Alpine tunnel on March 13th.
The accident killed 28 people and plunged Belgium, where most of the victims were from, into mourning.
The Lausanne hospital said the neurological situation of two of the girls who are suffering from multiple factures and concussion was "developing positively".
The third patient who is suffering from bone marrow lesions "is showing encouraging signs of recovery that allow some movement of fingers and toes", it added.
All three however will need to undergo an extended period of rehabilitation, the hospital said.
Swiss investigators are due to go to Belgium soon to hear again from the children who were on board the coach to try to find out what happened just before the accident, local prosecutor Olivier Elsig said.
He also said that technical experts were also trying to determine the state of the vehicle before it crashed.