The Pakistan Institute of Medical Sciences in Islamabad housed at least 15 newborns in the nursery when the fire broke out early on Wednesday, hospital officials said.
At least one baby was rescued, officials said, while federal Health Minister Mustafa Kamal confirmed at least 14 babies had died.
Rescue officials said the fire began about 6.45am after an air-conditioning unit compressor exploded inside the nursery in the gynaecology ward.
Firefighters quickly responded and extinguished the blaze and rescue teams began cooling operations at the site, local media reported. I
Islamabad Chief Commissioner Suhail Ashraf later said the fire had been extinguished and authorities were coordinating with the families.
Within hours, the Islamabad district magistrate appointed a multiagency fact-finding committee with directions to submit a report within 24 hours.
The panel will investigate the cause of the fire and its spread, determine whether adequate fire-safety measures were in place and evaluate the emergency response, a government notification said.
Interior Minister Mohsin Naqvi and Prime Minister Shehbaz Sharif expressed sorrow over the fire.
"A tragedy involving children is an irreparable loss," said Sharif, who ordered an immediate investigation.
President Asif Ali Zardari also offered condolences to the families, describing the deaths as "heartbreaking and an irreparable loss".
Zardari called for those responsible to be identified and dealt with under the law and urged hospitals to ensure effective fire-safety measures and emergency procedures, particularly in wards caring for newborns.
The deaths of the children sent a wave of shock and grief across the country.
Police were deployed at the hospital as grieving parents and relatives gathered, some weeping while others called for accountability and demanded answers about how the fire began and whether the nursery had adequate firefighting equipment.
Mohammad Sami said she gave birth three days earlier and her baby was receiving intensive care in the nursery when the fire erupted.
"I don't know what to say or whom to blame," she said through tears. "I have lost my child."
Hospital officials told families that the bodies would be released after the necessary paperwork was completed, Sami said.
Kamal, the health minister, told local Geo News channel that he was travelling from Karachi to Islamabad to personally oversee the investigation.
He said the director-general of health and the federal health secretary were already at PIMS, one of Islamabad's largest public hospitals, which recently was the site of a medical examination of imprisoned former prime minister Imran Khan.
Officials were in contact with the families, according to Kamal, who said the immediate priority was to support the parents and return the infants' bodies to them.
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