The words 'Price Tag', a slogan used by extremist Jewish settlers, were also scrawled on the walls of the Baptist Narkis Street Congregation in a quiet residential neighborhood in west Jerusalem.
"Officers are investigating a strong possibility of a nationalist motive but no one has been apprehended yet," police spokesman Micky Rosenfeld.
The graffiti also included profanity about Jesus, and the vandals slashed the tires of several cars parked in the church compound.
Two weeks ago, similar graffiti was scrawled on the 11th-century Monastery of the Cross which is also in west Jerusalem but no suspect have been arrested, Rosenfeld said.
Price Tag attacks have targeted mosques, Palestinian homes and Israeli military installations in the occupied West Bank.
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