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Israel's evacuation of the biggest hospital in Gaza represents an "insistence" on genocide, the Palestinian foreign ministry has said.

Hundreds of people evacuated Gaza City's Al-Shifa Hospital on foot on Saturday, an AFP journalist at the scene saw after the facility's director said the Israeli military ordered the site emptied.

While some wounded people, premature babies, and medical staff remained, columns of sick and injured – some of them amputees – displaced people, doctors, and nurses, made their way towards the seafront. Israel's army denied ordering the evacuation.

The Palestinian foreign ministry the evacuation "represents an official Israeli insistence on completing the episodes of execution and genocide against any Palestinian presence in Gaza City and the northern strip".

"This deepens the humanitarian and environmental catastrophe facing the strip," the ministry added.

"It is also a literal translation of the calls of extremist Israeli zealots who incite and demand the burning of Gaza, as they previously called for and practised in the burning of Huwara."

Huwara and other nearby occupied West Bank towns were subjected to a brutal settler attack in February, which an Israeli army commander described as a "pogrom".

The Israeli military denied ordering Al-Shifa to evacuate. It has claimed it "acceded to the request of the director of the Shifa Hospital to enable additional Gazans who were in the hospital, and would like to evacuate, to do so".

The UN estimated that 2,300 critically ill patients, staff, and displaced Palestinians were sheltering at the site before Israeli forces raided it on Wednesday.

It had at one point been a place of refuge for 60,000 displaced people.

Israel has sought and so far failed to provide evidence proving a Hamas headquarters is located beneath Al-Shifa since it overran the site.

Agencies contributed to this report.