Just before midnight in Senegal, Macky Sall announced on Twitter that 11 infants had died in the blaze.
"I have just learned with pain and dismay about the deaths of 11 newborn babies in the fire at the neonatal department of the public hospital," he tweeted.
"To their mothers and their families, I express my deepest sympathy," Sall added.
The tragedy occurred at Mame Abdou Aziz Sy Dabakh Hospital in the transport hub of Tivaouane, and was caused by "a short circuit", according to Senegalese politician Diop Sy.
"The fire spread very quickly," he said.
The city s mayor Demba Diop said "three babies were saved". According to local media, the Mame Abdou Aziz Sy Dabakh Hospital was newly inaugurated.
Health minister Abdoulaye Diouf Sarr, who was in Geneva attending a meeting with the World Health Organization, said he would return to Senegal immediately.
"This situation is very unfortunate and extremely painful," he said on radio. "An investigation is under way to see what happened."
The tragedy in Tivaouane comes after several other incidents at public health facilities in Senegal, where there is great disparity between urban and rural areas in healthcare services.
In the northern town of Linguere in late April, a fire broke out at a hospital and four newborn babies were killed. The mayor of that town had cited an electrical malfunction in an air conditioning unit in the maternity ward.
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