The move is the latest in Washington's effort to hobble the ICC, which has sought arrest warrants for Israeli officials over alleged war crimes in Gaza. The court has also pursued cases against Hamas leaders.
Secretary of State Marco Rubio designated Al-Haq, Al Mezan Centre for Human Rights, and the Palestinian Centre for Human Rights under an executive order targeting entities that assist ICC investigations into Israel.
"These entities have directly engaged in efforts by the International Criminal Court to investigate, arrest, detain, or prosecute Israeli nationals, without Israel's consent," Rubio said.
The United States, Russia, and Israel are among the nations that reject the ICC.
"We oppose the ICC's politicised agenda, overreach, and disregard for the sovereignty of the United States and that of our allies," Rubio said in a statement.
Last month, the US imposed sanctions on two ICC judges and two prosecutors, including those from allies France and Canada. In June, Rubio sanctioned four judges from the court.
"The United States will continue to respond with significant and tangible consequences to protect our troops, our sovereignty, and our allies from the ICC's disregard for sovereignty," Rubio warned.
Amnesty International condemned the US move as a "deeply troubling and shameful assault on human rights and the global pursuit of justice."
"These organisations carry out vital and courageous work, meticulously documenting human rights violations under the most horrifying conditions," said Erika Guevara-Rosas, a senior director at Amnesty.
She accused the Trump administration of seeking to "dismantle the very foundation of international justice and shield Israel from accountability for its crimes."
The ICC's prosecution charged Israeli Prime Minister Benjamin Netanyahu and former Israeli Defence Minister Yoav Gallant with war crimes and crimes against humanity in Israel's offensive in Gaza, including intentionally targeting civilians and using starvation as a method of war.
The Israeli war in Gaza has killed and wounded more than 220,000 Palestinians, 10 percent of the strip's 2.3 million population.
Last month, the United Nations officially declared famine in Gaza after a 23-month Israeli blockade on the entry of humanitarian aid to the strip.
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