The attack is the eleventh against a church since the High Court ruled in favour of allowing the Catholic Church's Herald newspaper to use "Allah" in its Malay-language section as a translation for "God".
In another incident, on the island of Borneo, police confirmed reports that they had found broken glass of what was reported to have been a rum bottle outside a mosque in Kota Samarahan, in Sarawak state.
"Broken glass was found outside a mosque. We are investigating. I do not want to say anything more," Ismail Omar, the deputy inspector of police, told AFP.
The Malaysian government has strongly criticised the attacks on churches, but has been accused of stoking Malay nationalism to protect its voter base after the opposition made unprecedented gains in 2008 elections.
In Geneva, the World Council of Churches said it was disturbed by the attacks and called on the Malaysian government to take immediate action.
About nine per cent of Malaysia's 28 million people are Christian, including 850,000 Catholics, most of whom come from indigenous groups in the Borneo states of Sabah and Sarawak.