Isaac Herzog told the BBC "everything is operating" at Al-Shifa, despite reports of no power.
"We deny this at all, there is a lot of spin by Hamas... but there's electricity in Shifa, everything is operating," Mr Herzog said.
Israel has said that Hamas has a base underneath the hospital building - a claim denied by Hamas.
Surgeon Marwan Abu Saada told the BBC on Saturday that the hospital had run out of water, food and electricity.
He said the sounds of shooting and bombardments echoed through the hospital "every second".
Israeli military spokesman Rear Admiral Daniel Hagari said Israel would help evacuate babies from Al-Shifa following a request from the hospital administration. A doctors group said on Saturday that two premature babies had already died.
Asked about growing calls for a ceasefire, including from France's President Macron, Mr Herzog asserted Israel's right to defend itself after the attacks of 7 October.
"We of course listen to our allies, but first and foremost, we defend ourselves," he said.
Be the first to reply to this url.