The baby boy reportedly born out of an incestuous relationship between an 11-year-old girl and her 14-year-old brother, has been taken into care.
Local social services chiefs have secured temporary guardianship of the five-day-old tot while his long-term future is decided, the Daily Mail reports.
The child mum has also been separated from her family including her older brother after leaving hospital in Murcia, south east Spain. She is now staying with a temporary foster family.
Her baby's whereabouts have not been disclosed, although local reports said he could be taken taken to a child protection centre or end up in emergency foster care or with extended family.
The measures have been taken while police await the result of DNA tests to confirm the siblings are the parents of the baby and social services bosses carry out their own independent investigation.
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.