An Israeli air strike hit the surgery department of Nasser Hospital in Khan Younis early on Tuesday.
Officials at the hospital said three people were killed and 10 injured.
The Israeli military said it had launched a precision strike on Hamas militants operating a command and control centre at the hospital.
It comes as Hamas on Monday released an Israeli-American soldier who had been held hostage in Gaza for more than 19 months, calling it a goodwill gesture towards the Trump administration.
