An Israeli court has charged Sheikh Raed Salah, leader of the northern branch of the Islamic Movement, with incitement to "terrorism" in connection with deadly unrest at a Jerusalem holy site last month, the justice ministry said.

Salah, a Palestinian citizen of Israel, was charged on Thursday in Haifa magistrates' court on a total of six counts, including support for a banned organisation.

His group was outlawed in 2015 for alleged incitement linked to the holy site, the al-Aqsa Mosque compound, known to Jews as the Temple Mount. The charges were denied by Salah and the Israeli decision to ban the movement remains contentious.

READ MORE: Islamic Movement rejects Israeli government ban

Thursday's statement by the justice ministry alleged that Salah issued "expressions of praise, sympathy or encouragement for an act of terrorism" on various occasions.

His alleged statements were made against "a special security background" in the wake of a July 14 attack in which three Palestinian citizens of Israel from Salah's hometown of Umm al-Fahm killed two policemen after emerging from the holy compound in occupied East Jerusalem.

The attackers were themselves shot dead by other officers.

The justice ministry quoted the charge sheet as saying Salah's statements were made at the Umm al-Fahm funeral of the assailants and in two sermons he delivered at Friday Muslim prayers in the town.

It said that the funeral was attended by thousands, some of them masked and chanting pledges to the dead attackers to "continue in your path."

It did not specify Salah's comments there.

Salah's lawyers and supporters say his sermons are always within the bounds of free speech and that he "stands against the murder of innocents".

They have called the 58-year-old preacher's arrest political intimidation and say it was intended to silence dissent.

Upon his arrest on August 15, Salah said his detention is "a political pursuit" and part of "pursuing the Arab people by the Israeli government".

Mohammed Barakeh, the chairman of the Higher Committee for the Arab citizens of Israel, told Al Jazeera that Salah's arrest "is a kind of anti-democratic act to put the Arab population in Israel under pressure".

READ MORE: Palestinians decry arrest of Islamic Movement leader

Israel responded to the July 14 attack by installing metal detectors and other security equipment at the entrance, but that triggered protests in which seven Palestinians were killed by Israeli forces.

As the unrest raged, a Palestinian broke into a home in a Jewish settlement in the occupied West Bank and stabbed four Israelis, killing three.

The crisis ended when Israel removed the security devices at the site, which includes the revered al-Aqsa mosque and the Dome of the Rock.

Salah's arrest followed his release from prison in January after serving a nine-month sentence on similar charges.

The holy site in the Old City is the third-holiest in Islam and the most sacred for Jews.