The latest incident occurred after three other churches were firebombed Friday, just days after a Kuala Lumpur court ruled non-Muslims to use the word "Allah" to refer to God in their literature.
Bishop Philip Loke said two firebombs were believed to have been thrown at his Good Shepherd Lutheran Church early Saturday but missed the glass windows, hitting the building wall instead.
He said church members discovered two burned patches on the wall at midday and found glass splinters on the ground. There was no damage to the three-story building in the Petaling Jaya suburb in central Selangor state.
"Why resort to violence? These attacks are a cowardly act and a crime against the Christian population," Loke told the Associated Press.
The Dec. 31 court decision incensed many Muslims, who see it as a threat to their religion. Hateful comments and threats against Christians have been posted widely on the Internet, but this is the first time the controversy has turned destructive.
Selangor police chief Khalid Abu Bakar said the attacks indicated the work of amateurs.
"We don't think the attacks were planned or coordinated. We believe they were carried out by hooligans or mischievous prankster trying to take advantage to stir the situation," he said.
Investigations are ongoing but there are no witnesses so far that could help in the probe, he said.
The court ruling followed a petition by Malaysia's Roman Catholic Church, whose main publication, the Herald, uses the word "Allah" in its Malay-language edition. The ruling also applies to the ban's broader applications such as Malay-language Bibles, more than 10,000 copies which were seized last year by authorities because they translated God as Allah.
The Herald says its Malay edition is read mainly by Christian indigenous tribes in the remote states of Sabah and Sarawak, who speak a variety of languages but pray mostly in Malay.
But the government contends that making Allah synonymous with God may confuse Muslims and ultimately mislead to them into converting to Christianity, a punishable offense in Malaysia despite a constitution that guarantees freedom of religion.