The baby, Rodrigo, was born on October 7 without a nose, eyes or part of his skull but the deformities were only discovered during his delivery at a hospital in Setubal, about 40 kilometres (24 miles) south of Lisbon.
Portugal’s Medical Council unanimously voted on Tuesday to suspend Dr Artur Carvalho from practising for six months.
The obstetrician has six other complaints against him, dating back to 2013.
The council opened an investigation after the parents of the deformed baby made a complaint and the birth made headlines.
“There is strong evidence” of the doctor’s negligence, which “may lead to a disciplinary sanction,” Alexandre Valentim Lourenco, medical council chief for the southern region told broadcaster RTP.
Given the impact of this case, which “has repercussions on the reputation of doctors” and “to reassure pregnant women”, he said the suspension was necessary to evaluate the complaints.
Caravalho had followed the pregnancy of Rodrigo’s mother in a private clinic in Setubal where he performed three mandatory ultrasounds but did not report any issues of concern.
The parents were alerted to a possible anomaly of the foetus after they requested a further ultrasound test in the sixth month of the pregnancy. but were reassured by the doctor.
“He explained that sometimes some parts of the face are not visible (on ultrasounds)… when the baby’s face is glued to the belly of the mother,” Joana Simao, the mother’s sister, told broadcaster TVI 24.
The baby is still at the paediatric wing of the hospital where he was born