Hishammuddin Hussein, the home minister, appealed for calm and moved to assure religious groups in the country that "they are safe".
"I take the events that happened last night very seriously," he said.
"We want to assure the public that this was not a co-ordinated and well-planned action."
A Malaysian court had last week overturned a government ban on non-Muslims using the word "Allah" in their literature, allowing Roman Catholic newsletter, the Herald, to use the term to refer to God in the Malay language.
The judge has since suspended the implementation of the ruling, after the government appealed and the Roman Catholic church agreed to the suspension.
|Police say they have stepped up security at churches following the two attacks [AFP]
Muslim groups held protests after prayers on Friday against the court overturning the "Allah" ban, despite a warning from Musa Hassan, the country's police chief, advising organisers to "let this be handled by the court" and that he "will take action against anyone who acts to jeopardise national security".
Muslims in Malaysia argue that the "Allah" is exclusive to Islam, and its use by Christians would confuse Muslims.
But Catholic church officials say that for Christian indigenous tribes in East Malaysia, who are the main readers of the Herald's Malay-language edition, "Allah" is the only word they have known for God for decades.
Al Jazeera's Harry Fawcett, reporting outside a mosque in the suburb of Kampung Baru, said that protests were held within the mosque compound.
"There was a lively crowd, but not a huge one. Some of the protest organisers filed complaints to local officials over the use of the word Allah in Christian literature," he said.
Najib Abdul Razak, Malaysia's prime minister, earlier said his government was powerless to stop the planned protests as long as protesters did not leave their mosques.
Marina Mahathir, a board member of the Sisters in Islam organisation and the daughter of the former prime minister Mahathir Mohamad, told Al Jazeera that many Malaysians are "deeply disappointed as to how this issue has been manipulated".
"This issue goes beyond words and debate. I think many do not understand aspects of this religion, which is why there has been a lot of misinformation going around," she said.
|A court ruling last week that the Herald may use the word 'Allah' has been suspended [EPA]
Fire in Friday's first incident gutted the administrative office on the first floor of the three-storey Metro Tabernacle church, shortly after midnight.
Mohamad Sabtu Osman, the Kuala Lumpur police chief, said a witness saw four people on two motorcycles breaking the glass front of the church and throwing an incendiary object inside before fleeing.
Molotov cocktails were believed to be thrown into the compounds of two other churches in Petaling Jaya, just outside Kuala Lumpur, before dawn on Friday.
The attacks on the Assumption church and the Life Chapel caused minor damage, officials said.
Osman said there were no fatalities in the attacks and police were investigating, but added that it was premature to link the attacks on the churches to protests by Muslim groups over last week's court ruling.
Lawrence Andrew, editor of the Herald, said many churches had employed extra security guards amid protest threats as a precaution for fear that matters "may just blow up".
And police say they have stepped up security at churches nationwide following the attacks.
Musa, the police chief, said he had "instructed all patrol cars to patrol all church areas - we are monitoring all churches".
Najib, the prime minister, condemned the attacks "because they will destroy our country's harmony".
"The government will take whatever steps it can to prevent such acts," he said.
Salahuddin Ayub, a leader from the Islamic opposition party PAS, also condemned the attack, saying Islam does not allow followers to destroy houses of worship belonging to non-Muslims.
"Even during war, those who seek sanctuary in houses of worship cannot be killed or the buildings itself destroyed," he was quoted as saying by the Malaysian Insider website.
Azmi Sharom, a columnist and law professor at Universiti Malaya, told Al Jazeera that "the unrest is not surprising because of the fact that the government has been pandering to these kinds of people for a long time".
He said the government allowed some groups to protest when others were banned because the main ruling Umno party - which depends on the Malay/Muslim demographic to remain in power - was "unwilling to do anything which would seem to go against what they think is the Malay/Muslim desire".
"This is a noisy demographic and it is potentially dangerous for Umno to alienate them, so this will be a real test for Najib's administration," he said.