The administrative offices of one church were destroyed by a firebomb attack and one of the other two churches attacked was slightly damaged. The government of the primarily Muslim nation has condemned the attacks on the churches and vowed to take action.
About 60% of Malaysians are Malay Muslims and the government relies on their vote. There also significant Chinese and Indian minorities, who are mainly Christians, Hindus and Buddhists.
The controversy stems from a ban on a Catholic newspaper, The Herald, using the word Allah: the Kuala Lumpur High Court struck down the three-year old ban on non-Muslims using of the word Allah.
Some major Muslim organisations, including the Islamic political party, PAS, have agreed with the court, saying other Abrahamic religions - Christinaity and Judiasm - may use the word, but some vocal groups, including the Muslim Youth Movement, Abim, have cast the use of the word Allah as a surreptitious effort on the part of Christians to try to seduce Muslims away from Islam.
The argument has continued in the media and the courts for months but had not become violent - until assailants on motorbikes were seen smashing the windows of the Metro Tabernacle Church, a Protestant church in Kuala Lumpur on Friday.
The ground floor office of the three-storey church was destroyed in a blaze a little after midnight, said Kevin Ang, a church spokesman.
Kuala Lumpur police Chief Mohamad Sabtu Osman said police had found a wrench, an empty petrol tin and two scorched motorbikes at the scene.
Separately, Molotov cocktails were thrown into the compounds of two other churches before dawn, causing minor damage in one and none in the other, church officials said.
Prime Minister Najib Razak condemned the attacks, saying such actions would "destroy our country's harmony".
The government will take whatever steps it can to prevent such acts," he said.
There was tight security at all churches in Malaysia and at several mosques where protests against the court's ruling took place, says the BBC's Jennifer Pak in Kuala Lumpur.
Mass nationwide demonstrations failed to materialise on Friday, but protesters at mosques in Kuala Lumpur carried placards reading "Allah is only for us" and "Heresy arises from words wrongly used".
"I hope the court will understand the feeling of the majority Muslims of Malaysia," said Ahmad Johari, at the National Mosque. "We can fight to the death over this issue."
The government has appealed against the court verdict and the High Court has suspended the decision's implementation until the appeal is heard.
And the guys in America are worried about gay marchers in Obama's inauguration parade. Priorities, anyone?