In a statement, Omar Shakir, the group’s senior director, described Yoav Gallant's statement as "abhorrent" and "collective punishment, which is a war crime."
"The International Criminal Court (ICC) should take note of this call to commit a war crime," he added.
On Monday, Gallant said his army is applying a complete siege on Gaza.
"I have ordered a complete siege on the Gaza Strip – there will be no electricity, no food, no fuel, everything is closed," he said.
Palestinian group Hamas launched Operation Al-Aqsa Flood against Israel early Saturday, firing a barrage of rockets and infiltrating Israel by land, sea, and air. It said the surprise attack was in response to the storming of Al-Aqsa Mosque in occupied East Jerusalem and growing settler violence against Palestinians.