The Sidang Injil Borneo Church in the central state of Negri Sembilan was the latest to be targeted amid anger over a court decision to overrule a government ban on Malaysia's minorities using "Allah" as a translation for "God".
The church attacks which erupted last Friday have sent tensions soaring in the multicultural nation, where the Muslim Malay majority lives alongside ethnic Chinese and Indian communities.
Home Ministry secretary-general Mahmood Adam, who briefed foreign diplomats on the crisis Monday, said they had asked why the term was off-limits when it is widely used by Christians in Indonesia and the Middle East.
"They don't understand the situation here, they just want to know why it can be allowed in other countries and not here," he told reporters.
"Be fair, you have to compare apples to apples, oranges to oranges. Our landscape is different from other countries. Malays here are different from (Muslims in) other countries.
"The landscape here is different from Indonesia so we can't compare," he said.
The row flared after the High Court on December 31 ruled in favour of the Catholic newspaper The Herald, which argued for the right to use "Allah" in its Malay-language section.
Malaysia's Christians say they have used the word without incident for centuries, but the ruling party -- which is vying for popularity among Muslims with the opposition Islamic party -- insists it must be used only by Muslims.
It argues that the use of "Allah" by Christians could cause confusion among Muslims and encourage religious conversion, which is illegal in Malaysia.
The ruling in the Catholic newspaper's favour was suspended last week pending an appeal, after the government argued the decision could cause racial conflict.
Since Friday, churches have been pelted with Molotov cocktails, splashed with black paint and had windows smashed with stones, triggering tighter security at places of worship nationwide.
Deputy state police chief Abdul Manan Mohamad Hassan confirmed Monday's attack on the Sidang Injil Borneo Church which conducts services in the national language, Malay.
"This morning I was alerted by a church member who saw the door of the church had been burnt," senior pastor Eddy Marson Yasir said. "It was very smoky inside the building but we are lucky that the fire didn't spread."
"We have been using the word 'Allah' during the service as most our church members speak the Malay language," he said of the 400-strong congregation which mostly hails from the eastern states of Sabah and Sarawak on Borneo island.
Despite the series of attacks, thousands of Malaysian Christians flocked to churches for weekly services Sunday.
Prime Minister Najib Razak has called for calm and said the government will not tolerate any threat to racial harmony.
Mahmood from the home ministry reiterated the government's condemnation of the church attacks and said Malaysia would do "all in our power" to protect religious freedom.
"These were not just attacks on houses of worship, they were attacks on the values and freedoms all Malaysians share," he said.
The row is one of a string of religious disputes in recent years that have strained relations between Muslim Malays and ethnic Chinese and Indians.
About nine per cent of Malaysia's 28 million people are Christians, including some 850,000 Catholics. More than half of Malaysia's Catholics are from indigenous groups, mostly from Borneo, and who mainly speak Malay.
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