Police said all three suspects are Jerusalem residents and that the investigation is ongoing. Investigators were expected to ask a court later Wednesday to extend their detention.
The first raid took place in Area A, after Palestinian police officers caught a 48-year-old Israeli in Bethlehem who possessed a large amount of pills suspected to be drugs.
National Security Minister Itamar Ben-Gvir had defended the IPS after the footage emerged, alleging that Tsarafi disrupted order and mistreated prisoners and staff.
The Israeli, Fares Abu al Hija, 32, of Kaukab Abu al Hija, is alleged to have conducted spying operations for Iran, including taking photographs of former defense minister Yoav Gallant's house.
The vandals broke into the synagogue sometime between the end of Kol Nidre on Sunday night and the beginning of services Monday morning and removed a Pride flag that was hanging in the sanctuary.
Dean Mor admitted to the charges against him, but claimed that he had felt threatened both at the church and by the officer at the police station.
The man, Hamdan Hamdan, is alleged to have been aware that the agent he was in contact with was Lebanese, and to have requested to be given security missions in Israel.
Former Wolfson doctor Aryeh Levin received six years in prison for rape and sexual offenses, despite prosecutors seeking a sentence of at least 13 years.
The charges cover preparation for a terrorist act involving explosives, a weapons offense for terrorist purposes, and receiving training or instruction for terrorist purposes.
The two officers had recently been deployed by the Sharet police station in the Ayalon District as part of an operation targeting drug-dealing hubs in the southern part of the city.
National Security Minister Itamar Ben-Gvir defended the Prison Service’s treatment of Tsarafi in a statement responding to the public defender’s criticism.