Israeli forces have ordered Palestinians sheltering at one of the last functioning hospitals in Gaza to evacuate from the complex, raising fears that troops will attempt to storm a facility crowded with thousands of people, some of whom have been shot at as they tried to flee, according to doctors there.

The Israeli military accused Hamas on Wednesday of conducting military activity inside the grounds of the hospital, the Nasser Medical Complex in Khan Younis, and alleged that the complex “was used to hold hostages.”

Israel’s claims could not be independently verified, but they signaled its intensifying focus on the hospital as Israeli forces try to root out Hamas fighters from the southern city. Previous Israeli warnings to evacuate hospitals, including Al-Shifa, the largest in Gaza, have often preceded military raids on the facilities.

“We demand the immediate cessation of all military activity in the area of the hospital and the immediate departure of military operatives from it,” the Israeli military said in a statement. It called for civilians sheltering at the hospital to leave for “safer spaces” in southern and central Gaza. The statement did not call on patients or medical workers to leave the hospital.

Gazans have said that Israeli forces regularly fire on areas where they have told people to flee, leaving nowhere in the enclave safe. Adding to the terror of those inside the hospital, Israeli forces fired on people who tried to leave the compound, with some being killed or injured, according to two doctors interviewed on Tuesday.

“The situation is very dangerous,” said Khaled Al-Serr, a general surgeon at the hospital. He said that the Israeli military had indicated just a day earlier that the hospital, which has been surrounded by Israeli ground forces for weeks, was safe.

Khan Younis has been a focus of Israel’s invasion of southern Gaza, with airstrikes killing hundreds of civilians and soldiers shooting people in the streets, according to the Gazan health ministry and Palestinian news media reports. Many Gazans who fled Israel’s military offensive in northern and central Gaza had sought shelter in Khan Younis, only to be forced to flee again as Israeli forces advanced deeper into the strip.

The Israeli military did not immediately respond to questions about the allegation that its forces had shot at those trying to flee.

Stéphane Dujarric, a spokesman for the U.N. secretary general, António Guterres, said on Tuesday that “intense fighting in Khan Younis, particularly near Nasser and Al Amal Hospitals,” continued to jeopardize the safety of medical staff.

The Israeli military says that Hamas uses hospitals as a cover for its operations, a claim that the group and medical officials have denied. Palestinians have sought shelter at hospitals even though Israeli forces have regularly launched strikes on and around them and in some cases raided hospital compounds.

Nahed Abu Taeema, the head of surgery at Nasser Hospital, said that explosions from airstrikes had grown closer to the hospital and more intense over the past few days. “But we won’t leave the hospital without our patients,” he said.

Many doctors and nurses, along with their family members who were sheltering at the hospital, had begun to pack their belongings and prepare to flee, Dr. Al-Serr said, even as leaving presented its own set of dangers.

There are about 8,000 people inside Nasser, he said, including badly wounded patients who have limb injuries and would be difficult to transport.

The situation inside the hospital has grown increasingly dire. Israeli strikes nearby caused fires that spread to the hospital’s medical equipment storage facility and supply warehouse, burning both nearly completely, said Dr. Ashraf Al-Qudra, the spokesman for the Gazan health ministry. Sewage has flooded into the emergency department, hindering the treatment of patients and threatening further spread of disease, he said.

Aaron Boxerman, Rawan Sheikh Ahmad and Farnaz Fassihi contributed reporting.

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