The attacks sharply escalated tensions in the Muslim-majority country ahead of planned protests later Friday against a Kuala Lumpur High Court verdict which struck down a 3-year-old ban on non-Muslims using "Allah" in their literature.
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.
The ruling was on a petition by the Herald, the main publication of Malaysia's Roman Catholic Church, which uses the word Allah in its Malay-language edition.
Only the first floor office in the three-story Metro Tabernacle Church was destroyed in the pre-dawn blaze, said Kevin Ang, a spokesman for the Protestant church. The worship areas on the upper two floors were undamaged and there were no injuries.
He quoted a witness as saying she saw three or four men on a motorcycle break the main glass front of the church and throw a gasoline bomb inside. The church occupies a corner plot in a row of shops in Desa Melawati, a suburb of Kuala Lumpur.
Separately, a Molotov cocktail was thrown into the compound of a Roman Catholic church before dawn Friday but caused no damage or injuries, said the Rev. Lawrence Andrew, the editor of the Herald.
Andrew said most churches have employed extra security guards amid the protest threats. "Most churches are taking precautions. They are aware it may just blow up," he said.
The government has appealed the court verdict and the High Court has suspended its decision's implementation until the appeal is heard.
Muslims argue that "Allah" is exclusive to Islam, and its use by Christians would confuse Muslims and tempt them to convert to Christianity.
Kuala Lumpur police Chief Mohamad Sabtu Osman told The Associated Press that it was premature to link the attacks on the churches to the protests over the lifting of the Allah ban.
"We are still investigating," he said. He also urged Muslims not to participate in the planned protests, adding that police would be stationed at mosques to monitor the situation.
About 60 percent of Malaysia's 28 million people are Malay Muslims, while the rest are ethnic Chinese, Indians and indigenou tribes who follow Christianity, Hinduism and other religions.
The Malay-speaking indigenous tribespeople, living in remote states of Sabah and Sarawak, are the main readers of the Herald's Malay-language edition. Catholic officials say "Allah" is the only word they know for God.
Many Muslims in Malysia have refused to accept the argument that "Allah" is an Arabic word that predates Islam, and that it is used by Christians in countries such as Egypt, Syria, Lebanon and Indonesia regularly in their worship.
The backlash against the court verdict has reinforced complaints by religious minorities in Malaysia that they face institutional discriminatio by the government.
On Thursday, the Malaysian judiciary's Web site was hacked and defaced with an apparent threat to Christians, The Star newspaper reported. The site, however, appeared to be normal on Friday.
The Star said the hacker, using the alias "Brainwash," defaced the site with a banner saying: "Mess with the best, die like the rest" and "Allah only restricted to Muslim only."