Prime Minister Benjamin Netanyahu said he mourns the fallen officer, "a lauded fighter." He said that "one day, the full tale of his heroism will be told. Israel's citizens owe him a huge debt."
The officer, whose name was not released for publication, was married with two children and a resident of northern Israel. His funeral will be held Monday at 3 P.M.
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Another Israeli soldier was moderately wounded in the operation.
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At least seven Palestinians were killed in Gaza after heavy fire was exchanged with Israeli forces, according to Palestinian sources, including a commander in Hamas' military wing. Hamas claimed that four of the casualties were part of its organization.
A statement by the Israeli army said that force was hurt during the first skirmish and that the shooting occurred while "the special force carried out a lengthy operation and encountered a very complex reality."
The military Spokesperson's Unit added that "What was revealed tonight is the very tip of operations that are carried out regularly and the purpose of which is to enable Israel's superiority as it exists today."
The statement said the commander's actions "will not be published in the media but he deserves our salute. His actions led to Israel having superiority over its enemies."
"I am stunned and I am grieving the loss of the IDF officer killed tonight," President Reuven Rivlin said. "I pray, together with all Israeli citizens, for the health of the wounded officer."
Defense Minister Avigdor Lieberman said: "The Israeli people lost an industrious fighter tonight, whose contribution to the state will remain confidential for many years." Education Minister Naftali Bennett said that "We send our condolences to the family and pray for the speedy recovery of the wounded. Thanks to heroes like these, we can all live here safely."
Former IDF Chief of Staff Benny Gantz said he knew the commander killed and the officer who was wounded. "We need to be proud for having such people," he said in an interview on Israeli army radio.