Washington on Wednesday condemned the deadly shelling of a UN shelter in south Gaza and reiterated calls for civilians to be protected during Israel's bloody war with Hamas.

The Gaza director of the UN agency for Palestinian refugees (UNRWA) said earlier Wednesday that two tank shells had hit a building sheltering 800 people in the southern city of Khan Yunis, with reports that nine people had died and 75 more injured.

"We deplore today's attack on the UN's Khan Yunis training center," State Department spokesman Vedant Patel said.

"You've heard me say it before, you've heard the Secretary say it before, but civilians must be protected and the protected nature of UN facilities must be respected," Patel told reporters.

Pressed on whether the United States was in contact with Israel about the attack, Patel declined to go into the details of the conversations, but said: "We intend to continue to have these conversations with the Israeli government and raise these very tough and difficult situations."

"Humanitarian workers must be protected so that they can continue providing civilians with the lifesaving humanitarian assistance that they need," said Patel.

The Israeli army said Tuesday it had "encircled" Khan Yunis, Gaza's main southern city which has become the epicenter of recent fighting.