The ministry said power was cut off and the generators stopped after the raid at the Nasser Hospital in the main southern city of Khan Younis, leading to the deaths of five patients.
In recent days, intense fighting has raged in the vicinity of the hospital — one of the Palestinian territory's last remaining major medical facilities still operational.
The Israeli army said its forces at the hospital had taken into custody more than "20 terrorists" suspected of involvement in Hamas's October 7 attack that sparked the war.
Troops entered the hospital on Thursday, acting on what the military said was "credible intelligence" that hostages seized in the attack had been held at the facility and that bodies of some may still be inside. It later acknowledged it had found no evidence.
A witness, who declined to be named for safety reasons, told AFP the Israeli forces had shot "at anyone who moved inside the hospital."
Gaza's health ministry also raised fears for four other patients in the intensive care unit and three children, saying it held Israel "responsible for the lives of patients and staff considering that the complex is now under its full control."
Palestinians mourn over the body of a victim following Israeli bombardment on Rafah in the southern Gaza Strip, at al-Najar hospital on Friday February 16, 2024, amid ongoing battles between Israel and the Palestinian militant group, Hamas.
'Pattern of attacks'
Doctors Without Borders, an international humanitarian NGCO, said its medics had been forced to flee and leave patients behind, with one employee unaccounted for and another detained by Israeli forces.
Roughly 130 hostages are still believed to be in Gaza after Hamas's October 7 attack on Israel, which resulted in the deaths of about 1,160 people, mostly civilians, according to an AFP tally based on official Israeli figures.
Dozens of the estimated 250 hostages seized during the attack were freed in exchange for Palestinian prisoners during a week-long truce in November last year. Israel says 30 of those still in Gaza are presumed dead.
At least 28,775 people, mostly women and children, have been killed in Israel's assault on Gaza, according to the Hamas-run health ministry.
Israel has repeatedly accused Hamas militants of using hospitals for military purposes, something Hamas denies.
The UN Human Rights Office said Israel's raid on the Nasser Hospital appeared to be "part of a pattern of attacks by Israeli forces striking essential life-saving civilian infrastructure in Gaza, especially hospitals."
At a press briefing Friday, World Health Organization spokesman Tarik Jasarevic said the UN agency was trying to get access to the hospital.
'Dying slowly'
The Israeli army reported the death of another soldier in Gaza, raising the number killed in the ground operation to 234.
It said it had carried out "targeted raids" overnight and killed "12 terrorists" in Khan Younis.
The Gaza health ministry said that another 112 people had been killed in strikes across the territory.
Around 1.4 million displaced civilians are trapped in the town of Rafah, after taking refuge in a makeshift encampment hard by the Egyptian border with dwindling supplies.
"They are killing us slowly," said displaced Palestinian Mohammad Yaghi.
"We are dying slowly due to the scarcity of resources and the lack of medications and treatments."
At the Abu Yussef Al-Najjar Hospital in Rafah, AFP saw several corpses lined up in body bags as relatives grieved nearby.
U.S. President Joe Biden urged Israeli Prime Minister Benjamin Netanyahu late Thursday not to carry out an offensive on Rafah without a plan to keep civilians safe, the White House said.
But Netanyahu has insisted he will push ahead with a "powerful" operation in Rafah to achieve "complete victory" over Hamas.
The Wall Street Journal reported Thursday that Egypt was building a walled camp near the border to accommodate any Palestinians displaced from Gaza, citing Egyptian officials and security analysts.
The UN has stressed an exodus of Gazans into Egypt must be "avoided at all costs."