The fire early on Wednesday was confined to the third-floor nursery and did not affect the rest of the facility.
Hospital officials said the fire spread so quickly the two doctors, two nurses and other staff present were able to rescue only one baby among the 15 in the nursery.
The scene at the Pakistan Institute of Medical Sciences in Islamabad was sombre on Thursday as doctors, staff, patients and relatives mourned the newborns.
Access was restricted to the third-floor area where the fire occurred.
Witnesses, including relatives of other patients, said they saw the family of the only baby to survive the fire leave the hospital with him after the blaze broke out.
Prime Minister Shehbaz Sharif appointed the investigating committee, led by retired federal secretary Shahid Khan.
The committee is expected to make urgent recommendations to Sharif within 48 hours and deliver a comprehensive report within five days.
Hospital and district officials initially said an exploding air-conditioning unit caused the fire.
In its preliminary report, however, the hospital said a blast involving a nebuliser sparked the blaze, which spread within minutes because of the high concentration of oxygen in the nursery.
The committee had not reached its own conclusion and would independently determine the cause, the city administration said.
Officials said authorities handed over the bodies of all 14 newborns to their families for burial on Wednesday night.
The Pakistani Taliban, a militant group also known as Tehrik-e-Taliban Pakistan, or TTP, expressed grief over the newborns' deaths and offered condolences to their families.
The group has been behind numerous deadly attacks on security forces and civilians across the country in recent years.
The deaths prompted authorities to order broader reviews of fire-safety measures and firefighting equipment at hospitals.
In Punjab, Pakistan's most populous province, the government instructed the health department to immediately review fire-safety systems and emergency-response facilities, according to a government statement.
Sharif dismissed Health Secretary Aslam Ghauri, the health mMinistry's highest-ranking civil servant, after the fire.
Grieving parents and members of civil society have demanded answers about how the fire began and whether the nursery had adequate firefighting equipment.
The UN children's agency, UNICEF, said it was saddened by the deaths and called for an urgent review and strengthening of fire-prevention and safety standards at health facilities.
