Senegal's President Macky Sall fired his health minister on Thursday as his country mourned the death of 11 newborn babies in a hospital fire blamed on an electrical short circuit.

The tragedy late Wednesday in the western city of Tivaouane was just the latest in a series of hospital deaths that have exposed the weaknesses of the nation's healthcare system.

Sall earlier announced the tragedy on Twitter and declared three days of national mourning.

"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 wrote.

"To their mothers and their families, I express my deepest sympathy."

Outside the Mame Abdou Aziz Sy Dabakh Hospital in Tivaouane, a city with a population of 40,000, one of the distraught mothers called out for her son.

"Where is Mohamed?" she cried.

Her baby son was taken to the hospital 10 days ago and was baptised on Monday, Mohamed's 54-year-old father Alioune Diouf said.

The city's mayor Demba Diop said the fire had been caused by a short circuit and spread very quickly.

He denied allegations from relatives at the hospital and across social media that the babies had been left alone, saying a midwife and nurse were present on Wednesday evening.

"There was a noise and an explosion that lasted three minutes at most," he said outside the hospital entrance.

"Five minutes after, the fire brigade arrived. People used fire extinguishers."

The mayor said the air-conditioning had accelerated the flames and added that the two nurses fainted but were revived.

"There was no negligence," Diop insisted.

The disaster however sparked calls for the resignation of Health Minister Abdoudaye Diouf Sarr, who was quoted in media reports also as blaming an electrical fault.

The presidency in the evening said he would be replaced by Marie Khemesse Ngom Ndiaye, formerly the director-general of the public health authority.

Sall would return early from abroad and visit the hospital on Saturday, his office said.

The maternity unit was equipped to take care of 13 babies.

Map of Senegal locating the city of Tivaouane, where 11 newborn babies died in a hospital fire on Wednesday.
Map of Senegal locating the city of Tivaouane, where 11 newborn babies died in a hospital fire on Wednesday. AFP / Tupac POINTU

"At the time of the fire, there were 11 whom nurses were unable to save," the minister said.

World Health Organization chief Tedros Adhanom Ghebreyesus tweeted that he was "beyond heartbroken with this tragic news.

"I'm sending my deepest condolences to the parents and families of the babies who lost their lives."

Outgoing health minister Sarr, who had been in Geneva attending a meeting with the WHO, said an investigation is under way.

The tragedy in Tivaouane comes after several other public health incidents in Senegal, which suffers from a 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 town's mayor cited an electrical malfunction in an air-conditioning unit in the maternity ward.

Wednesday's accident came over a month after the nation mourned the death of a pregnant woman who waited in vain for a caesarean section.

The woman, Astou Sokhna, arrived at a hospital in the northern city of Louga in pain. The staff refused to accommodate her request for a C-section, saying it was not scheduled.

She died on April 1, 20 hours after arrival.

Sokhna's death caused a wave of outrage across the country over the dire state of the health system. Sarr acknowledged two weeks later that the death could have been avoided.

Three midwives on duty the night Sokhna died were given a six-month suspended prison sentence on May 11 by the High Court of Louga for "failure to assist a person in danger" in connection with her case.

Amnesty International's Senegal director Seydi Gassama said his organisation had called for an inspection and upgrade for neonatal services in hospitals across Senegal after the "atrocious" death of the four babies in Linguere.

With the new tragedy, Amnesty "urges the government to set up an independent commission of inquiry to determine responsibility and punish the culprits, no matter the level they are at in the state apparatus", he tweeted.

"More babies burned in a public hospital... this is unacceptable @MackySall," he tweeted.

"We suffer with the families to whom we offer our condolences. Enough is enough."