Malaysia's premier called for calm on Saturday, in a visit to one of the damaged churches.
Tensions were heightened last week when the High Court ruled in favour of the Catholic Herald newspaper which has used "Allah", a word that is used by Muslims around the world.
Two more churches and a Catholic convent school in Malaysia have been targeted by would-be arsonists.
Police said there were no reports of injuries in Sunday's incidents, which brought the total number of churches attacked since Friday to six.
Prime Minister Najib Razak on Saturday sought to quell tensions in the multicultural nation.
"Islam prohibits us from insulting or destroying any other religions, either in the physical form or in the form of their worship places," Najib said.
"All parties need to stay calm and should not act emotionally."
On Sunday, Malaysians packed churches to listen to sermons of "reaching out in friendship to all, including Muslims" and "keeping the peace in multi-religious Malaysia".
Police in the city of Taiping, around 300 km (185 miles) from the capital Kuala Lumpur, said a petrol bomb was thrown at the guard house of a Catholic convent school but failed to go off.
They also said they had found several broken bottles including paint thinners outside one of the country's Anglican churches, All Saints, Taiping, and said one of the building's walls had been blackened.
However, the ruling was suspended on Wednesday pending an appeal, after the government warned the decision could cause racial conflict.
Muslims say that they need to defend their religion.
The newspaper wants to use the word "Allah" to describe the Christian God, but Muslims say Christian missionaries will use the word a tool to confuse and convert Muslims.
Malaysia is mainly Muslim and Malay but there are ethnic Chinese and Indian minorities who mainly practise Christianity, Buddhism and Hinduism. Around 9 percent of the 28 million Muslim population are Christian, including 800,000 Catholics.
Related news reports:Güncelleme Tarihi: 10 Ocak 2010, 15:54