The Israel Defense Forces (IDF) said in a statement that "precise operations" were launched targeting the hospital.
Hamas militants were killed in close-quarters combat, and the Israeli army located weapons in the area "while avoiding harm to civilians, medical staff, and medical equipment," noted the statement.
In the area of Al-Qarara in Khan Younis, the Israeli army killed Palestinian militants and destroyed infrastructure, including one from which anti-tank missiles were launched at Israeli troops two days ago, the statement added.
The IDF began its raid on Al-Shifa Hospital early Monday.
The hospital, the largest one in the Gaza Strip, has been previously targeted by the Israeli Army.