Video footage shared with Al Jazeera showed crowds of displaced people, who had been sheltering inside the hospital, leaving on Wednesday. A doctor wearing green hospital scrubs walked ahead of the crowd, and some carried white flags.

Israeli forces ordered the evacuation of the complex on Tuesday. In a post shared on the social media platform X on Wednesday, the army said, “Hamas continues to conduct military activities” in the hospital, an unsubstantiated claim Israel has made about other Gaza health facilities it has raided during its months-long war.

The Israeli military – which used drones and loudspeakers to tell people to leave Nasser Hospital – said it opened “a secure route” to allow civilians to exit, while medics and patients could remain inside.

However, witnesses and medical NGO Doctors Without Borders (Medecins Sans Frontieres, or MSF) said those sheltering inside were afraid to leave after reports people were shot on the way out. The Israeli army also fired on people inside the hospital, including a doctor and a nurse.

More than 2,500 people are still inside the complex, including displaced people, patients, medics and their families, Gaza Health Ministry spokesperson Dr Ashraf al-Qudra said late on Wednesday.

The situation at the hospital was already critical but the last 24 hours have made things on the ground even more “scary”, MSF’s Guillemette Thomas told Al Jazeera.

“The situation is really critical for the patients and we are worried about the future,” she said. About 400 patients are in a critical condition at the hospital, she added.

World Health Organization spokesperson Tarik Jasarevic said Israel has denied the UN agency access to Nasser Hospital since January 29.

“We tried several times to go there, but our requests have been denied. We heard reports about some 400 patients still being there, that 10 people have been killed, that a warehouse has been destroyed,” he told Al Jazeera.

‘They opened fire’

Dr Ahmed al-Moghrabi, the head of plastic surgery at Nasser Hospital, recorded a message from inside the facility when Israel’s evacuation orders came in.

“[The Israeli army] sent a hostage with cuffed hands into the hospital asking him to tell us that we should evacuate. And when people started really evacuating, they opened fire and they shot at the people. And they killed the hostage [they had sent inside], as well,” he said.

Speaking to Al Jazeera late on Wednesday, he said thousands of people, including critically ill patients, are being delayed at Israeli checkpoints as they try to flee the area. He also described the situation at the hospital as “dangerous”.

Nasser Hospital, the largest health facility in southern Gaza, has been under siege for three weeks. The bodies of several people killed by Israeli sniper fire in the hospital compound have been lying on the ground for days as it is too unsafe to reach them.

At least three people have been killed by Israeli snipers near the facility in the past 48 hours, according to the Palestinian health ministry.

Al Jazeera’s Tareq Abu Azzoum, reporting from the city of Rafah on Wednesday, said Israeli forces have been setting up checkpoints along the road leading to Nasser medical facility as they force people to flee.

“The situation, on an hourly basis, is getting much more difficult and dire for people who are trapped inside this medical facility,” he said. “Some people [who left], exposed to Israeli fire, were forced to return back again to the medical facility.”

Earlier, Al Jazeera’s Hani Mahmoud said Israeli forces destroyed one of the main gates of the facility.

“They destroyed the northern gate of the hospital and blocked it with piles of sand and rubble. Only the eastern gate is open now,” he said, also reporting from Rafah.

“There are tanks and armoured vehicles stationed in front of that gate. There are face-recognition cameras installed … From past experience, setting up face-recognition cameras and hi-tech equipment means raids and mass arrests are soon going to happen,” he added.

Israeli forces have raided Gaza’s hospitals one after the other since the war, which has killed more than 28,000 Palestinians, began on October 7.

In just the first 36 hours of the war, Israel targeted Nasser Hospital, as well as the Indonesian Hospital and al-Quds Hospital, killing dozens of healthcare workers. By the end of November, 30 of Gaza’s 36 hospitals were hit by Israeli rockets. Currently, only six of Gaza’s hospitals remain functional.