Israel’s strikes on a major hospital in southern Gaza on Tuesday, in a bid to kill a top Hamas commander, have drawn new attention to one of the war’s most contentious issues: Israeli attacks on medical facilities, and Hamas’s use of such sites for military purposes.

The attack on the European Gaza Hospital complex near Khan Younis killed at least six people, according to the Gazan medical authorities, and left several deep craters in and around the hospital grounds, according to video filmed at the site and verified by The New York Times.

In a separate set of attacks, Israeli strikes killed dozens of people in northern Gaza overnight, Palestinian health officials said on Wednesday.

Even in a war that has decimated Gaza’s health sector, Israel has rarely launched as powerful an attack on a health complex as the one that damaged the European Gaza Hospital on Tuesday.

The Israeli military said it had been targeting a Hamas command center underneath the complex, and Israeli officials who spoke on condition of anonymity to divulge sensitive details said the specific target was Muhammad Sinwar, the senior Hamas commander.

Imad al-Hout, the hospital’s director, said in a phone interview that the strikes — which he said were conducted without warning — had damaged walls and pipes, cut off the water supply, put the hospital out of service, and forced most of the 200 patients to evacuate. Dr. al-Hout denied that Hamas fighters operated inside the hospital complex, adding that he did not believe the group had dug tunnels beneath it, though he could not definitively rule it out.