Left-leaning daily Haaretz earlier quoted unnamed soldiers as saying commanders ordered troops to shoot at crowds near aid distribution centres to disperse them even when they posed no threat.
The allegations followed repeated reports by eyewitnesses and local authorities over recent weeks of deadly incidents around aid distribution centres in the territory, where Israeli forces are battling Hamas militants.
Haaretz said the military advocate general, the force's top legal authority, had instructed the force to investigate "suspected war crimes" at aid sites.
When asked by AFP, the Israeli military declined to comment on that particular claim.
Netanyahu said in a joint statement with Defence Minister Israel Katz said Israel "absolutely rejects the contemptible blood libels" and "malicious falsehoods" in the Haaretz article.
The military said in a separate statement that it "did not instruct the forces to deliberately shoot at civilians, including those approaching the distribution centres".
It added that Israeli military "directives prohibit deliberate attacks on civilians."
After more than 20 months of devastating conflict, rights groups say Gaza's population of more than two million faces famine-like conditions.
The health ministry in Hamas-ruled Gaza says more than 500 people have been killed near aid centres since late May, when a new US- and Israeli-backed foundation began distributing aid.
The privately run Gaza Humanitarian Foundation denies that deadly incidents have occurred in the immediate vicinity of its aid points.
Netanyahu and Katz added in their statement: "The soldiers of the (Israeli military) receive clear orders to avoid harming innocents -- and operate accordingly."
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