Israeli forces, who left the hospital in Gaza City on Monday after a two-week operation, detained hundreds of suspected Palestinian fighters and left a swathe destroyed buildings in their wake.
"The people who need medical evacuation will increase, and medical evacuation is already slow," said WHO Director-General Tedros Adhanom Ghebreyesus.
"People will die because they will not get the services either from Shifa or because of slow evacuation, because they cannot be evacuated."
Israel said it killed hundreds of Hamas fighters who had based themselves there. Hamas and medical staff deny fighters were present.
"The process for the evacuation has to be expedited," he said. "Otherwise we will lose many people. We will lose many lives."
Richard Peeperkorn, WHO Representative for the West Bank and Gaza, said the destruction of Al Shifa Hospital would leave "thousands without healthcare." He said patients would have to somehow be moved to other healthcare facilities in the north of the war-torn Palestinian enclave, which are already struggling to remain functional.
"We have to recognise that absolutely insufficient healthcare is provided in Gaza," he said. "It's a health system on its knees as we said so often ... It's insufficient. It's incomplete."
Only 10 of Gaza's 36 hospitals are still able to function even partially, Tedros said.
He said WHO was seeking to visit the place where Al Shifa stood to speak to staff and see what could be saved, but that the situation on the ground looked "disastrous".
Al Shifa, the Gaza Strip's biggest hospital before the war with 750 beds and many operating rooms, was one of the few healthcare facilities that had been partially operational in the north of Gaza before the raid.
