Medical teams had buried on the grounds of the hospital 13 patients who had died because the facility had no power or oxygen, Gaza's health ministry said.
The WHO says the hospital in Khan Younis, which is Gaza's second-largest and is crucial to the territory's crippled health services, stopped working last week after an Israeli siege followed by a raid.
The WHO and partners have so far carried out three evacuations from the hospital, the latest on Wednesday, transferring a total of 51 patients to southern Gaza, the U.N. agency's Ayadil Saparbekov told a press briefing.
"The WHO will continue to try evacuation of those critically ill and critically wounded patients from the Nasser hospital to other hospitals in the south, including the field hospitals that have been established in Rafah," Saparbekov said.
"However it's a very difficult and high-risk mission."
Israeli forces had withdrawn from the hospital, positioning themselves nearby and preventing movement to and from it before storming it once more, the Gaza health ministry said. There was no immediate comment from Israel.
The number of patients remaining in Nasser hospital had been changing by the hour as some people left to escape the fighting and others succumbed to their wounds, Saparbekov said.
Gaza's health ministry had said in an earlier statement on Wednesday that 110 patients were waiting to be evacuated. It said eight patients at Nasser had died due to the lack of power and oxygen four days previously and that their bodies had begun to decompose, posing a risk to other patients.
When the WHO carried out the evacuations so far, it observed four doctors and nurses at Nasser hospital along with about a dozen volunteers helping medical staff keep patients alive, Saparbekov said. Staff had not yet managed to reconnect the main generator.
The Gaza health ministry said there was a lack of food, drinking water and medical supplies at the complex, and that the ground floors were flooded with sewage water.
Four-and-a-half months after Israel began its campaign in Gaza in retaliation for a major Hamas attack on southern Israel on Oct. 7, just 13 of the Palestinian enclave's 34 hospitals are functioning on a partial or minimal level.
Gaza's population of 2.3 million faces acute hunger and the spread of disease in a humanitarian crisis that aid officials describe as unprecedented.
Most Gaza residents have been displaced and are crammed into the south of the strip around Rafah, close to the border with Egypt.
Israel says Hamas, the Islamist group that has run Gaza since 2007, uses hospitals for cover. Hamas denies this and says Israel's allegations serve as a pretext to destroy the healthcare system.