The ministry said dozens of bodies had been found at the complex, where a journalist and eyewitnesses saw tanks and vehicles pulling out.
Eyewitnesses said dozens of air strikes and shells had hit the area around the complex.
The government media office in Gaza said the Israeli air strikes had provided cover for the withdrawing vehicles.
Gaza’s civil defence and medical authorities are heading to al-Shifa Hospital for recovery operations following the Israeli withdrawal, says Moath al-Kahlout, reporting from Gaza’s northern city of Jabalia.
There is “confirmed news” that the buildings of the complex and medical machines inside the hospital “are totally destroyed”, al-Kahlout said.
Dead bodies are scattered in the street near the hospital, he added.
At one point, 107 patients were stuck inside the human resource development building, “which is not prepared at all for medical care”.
UNICEF Regional Director for the Middle East Adele Khodr says Gaza is not just a humanitarian crisis but a “moral” one.
“It is a test for our humanity and ability to save the children’s lives,” she said on X, adding that it “will have a consequence on the future”.
