Security forces raided offices of the non-governmental groups in the West Bank, confiscating computers and equipment before sealing off entrances, Palestinian witnesses and officials said.
The Israeli military said the groups were used by the Popular Front for the Liberation of Palestine (PFLP), a group it has designated a terrorist organisation. Israel has previously declared six of the groups as terrorist organisations.
The designation, which has drawn criticism from the United Nations and human rights watchdogs, was ratified on Wednesday for three of them. The United Nations called for the designations to be revoked.
"Despite offers to do so, Israeli authorities have not presented to the United Nations any credible evidence to justify these declarations," the UN Human Rights Office said in a statement. "As such, the closures appear totally arbitrary."
The U.S. State Department said Israel had told the United States it would provide more information on the reasons behind the decision to close the organizations after Washington contacted Israeli officials.
"We will review what is provided to us and come to our own conclusion," State Department spokesperson Ned Price said.Nine European Union countries have said they will continue working with the groups, citing a lack of evidence for the Israeli accusation.
The UN identified the groups as the Addameer Prisoner Support and Human Rights Association; Al Haq; Bisan Center for Research and Development; Defense for Children International – Palestine; Health Work Committees (HWC); Union of Agricultural Work Committees (UAWC); and the Union of Palestinian Women's Committees (UPWC).
Israeli Defence Minister Benny Gantz reiterated Israel's claim that the organisations had operated undercover to serve the PFLP, which has carried out deadly attacks on Israelis and which the United States and the EU regard as a terrorist organisation.
"They also assist in raising funds for the terrorist organisation via a variety of methods that include forgery and fraud," Gantz said.
Palestinian officials condemned the move, which Prime Minister Mohammad Shtayyeh said was invalid.
"These are legal institutions that work under the law," Shtayyeh told reporters during a visit to the office of Al-Haq in Ramallah.
Earlier, Palestinians clashed with Israeli forces arriving to guard Jewish worshippers visiting Joseph's Tomb, a shrine in the West Bank city of Nablus. The site has seen repeated clashes between Palestinians and Israeli forces.
An 18-year-old Palestinian, who the Israeli military alleged had shot at soldiers, was killed and at least 30 people were wounded during the clashes in Nablus, Palestinian medics said.