The evacuation came as Israel said it was stepping up operations against Hamas militants and mediator Qatar said only "minor" obstacles remained to getting agreement on the release of hostages.
Sirens blared across Jerusalem to warn of rocket fire from Gaza, sending civilians scurrying for cover as loud blasts from intercepted missiles pierced the air.
In Gaza, a lack of fuel to power incubators has previously led to the deaths of other vulnerable newborns at Al-Shifa hospital, according to the Hamas-run health ministry in the territory.
Al-Shifa has become the focus of the six-week-old war that began October 7 when Gaza-based Hamas militants stormed across the militarised border to kill, according to Israeli officials, around 1,200 people and take roughly 240 hostages.
In Gaza, the Hamas government says 12,300 have been killed in Israel's relentless aerial bombardment and ground operations in retaliation for the worst-ever onslaught against the country.
Most of the casualties on both sides are civilians.
WHO chief Tedros Adhanom Ghebreyesus said 31 "very sick" babies were moved in a joint operation with staff from the UN and the Palestinian Red Crescent Society (PCRS), which used six ambulances in the transfer.
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