Molotov cocktails were hurled at the All Saints church and the school in Taiping in Perak state.
"There were black marks on the wall [of All Saints]. We believed there was a small fire earlier but there was no damage as the wall was intact," Zulkifli Abdullah, the state police chief, said.
He said a broken bottle filled with the inflammable liquid paraffin was found inside the compound of St Louis Catholic Church.
Muslims protesting
Muslim groups have staged protests in response to a court ruling last week that gave a Catholic newspaper the Herald the right to print the Arabic word for God, Allah, following a long-running dispute with the government over the issue.
Thousands of Malaysian Christians turned up to Sunday services, despite the recent tensions.
Four churches in the Kuala Lumpur area have been hit by firebombs since Friday, leaving one badly damaged with its ground floor gutted, and prompting Najib Razak, the prime minister, to promise to crack down on race crime.
Hermen Shastri, secretary-general of the Council of Churches, said officials had stepped up security in the wake of the attacks.
"The attacks show they are more just a prank as it does not appear to be a major [attack], someone is trying to send a signal that they are unhappy," he said.
The word Allah has been used by Malay-speaking Christians for centuries, as well as by Christians in Arabic-speaking countries and in Indonesia.
Rev Lawrence Andrew, editor of the Herald, has said there is no other appropriate term for God in Malay.
About 10 per cent of Malaysians are Christians, including about 850,000 Catholics. Around 60 per cent of the population are Muslims.
