The Palestinians announced a fresh push against Israel at the International Criminal Court on Tuesday, a day after the United States said it was closing their Washington mission partly over the campaign.
"The US made the correct decision when it chose to close the PLO offices in Washington", he told members of his cabinet.
Bolton also said the ICC had informed the US that it will soon open a "formal investigation" into possible war crimes and crimes against humanity committed by USA troops in Afghanistan.
If such a probe proceeds, the Trump administration will consider banning judges and prosecutors from entering the United States, put sanctions on any funds they have in the US financial system and prosecute them in the American court system.
In recent weeks, the United States has cut more than $200 million in bilateral aid to the Palestinians as well as cancelled its support for the UN agency for Palestinian refugees. Jordan, a USA ally, said the decision would only fuel radicalism and harm prospects for Middle East peace.
President Donald Trump is closing the Palestine Liberation Organization's mission in Washington, the latest US blow against the Palestinians and an worldwide court during the stalled Mideast peace process.
Trump also recognized Jerusalem as Israel's capital and moved the U.S. Embassy there, from Tel Aviv.
The PLO office in Washington has always been the focus of controversy.
In making such moves, Trump has sided with Israel on core issues in the conflict without publicly asking for any concessions in return.
Senior diplomat Dr. Saeb Erekat demanded the global community to intervene in what he argued were USA "attacks against the worldwide system as a whole" to defend Israel.
The Palestinian leadership is weighing retaliatory measures against United States penalties, including halting security cooperation, a senior Palestinian official said Wednesday.
"The Palestinians don't want to negotiate with us, and at the same time incite violence towards Israel", he added.
Germany, France, Italy, Spain and Britain called on Israel not to raze the Bedouin village of Khan al-Ahmar in the occupied West Bank after Israel's top court on Wednesday cleared the way for its demolition. Khan al-Ahmar is situated outside Jerusalem between two Israeli settlements.
Erekat stressed that the Palestinians are committed to the peace process on the basis of the two-state solution, but will not accept the current USA administration team to be the peace mediator.
The court has been hobbled by the refusal of the U.S., Russia, China and other major nations to join.
Agriculture Minister Uri Ariel (Jewish Home) called the measure a "New Year's gift" to Israel and the Jewish people.