The child mum could end up being separated from her family permanently if it is felt any return home would put her well-being seriously at risk, otherwise she would be allowed back with social service supervision.
News of the birth was made public on Monday.
Regional Health authority boss Manuel Villegas has described the case as 'absolutely exceptional.'
The siblings, both Bolivian immigrants, have been questioned by detectives along with their family who told police they had no idea the child mum was pregnant and confirmed the older brother is the dad.
Respected Spanish daily El Mundo said the youngster was 10 when she fell pregnant, but nothing untoward was discovered by a paediatrician who examined her when she sought medical help for stomach pains.
Her parents are said to have called for an ambulance to take her to hospital from their home in the centre of Murcia last Friday thinking she was suffering a 'serious stomach problem.'
She gave birth at the city's Virgen de la Arrixaca Hospital in Murcia shortly after being admitted.
Officials have confirmed the girl's brother, who was 13 when the newborn baby was conceived, will not face prosecution as he is under the age of criminal responsibility in Spain.
Police sources say there is no evidence at this stage pointing to the sibling pair having anything other than consensual sex.
Local reports say the child mum was a good student who attended school regularly and did not come from a 'dysfunctional' family.