Malay-speaking Christians prayed and sang hymns using the Arabic word, a practice they have observed for hundreds of years but now the focus of an increasingly tense religious row in the Southeast Asian nation.
"They all contain the word 'Allah'," a pastor at a church near the capital Kuala Lumpur said of the songs sung by his congregation.
"(The Malay-language Bible) contains the word 'Allah'. When we preach we have to read the text. It's a really difficult situation," he added, speaking on condition of anonymity due to the passions surrounding the issue.
Islamist leaders in the country say "Allah" -- which also is used by Malay Muslims to refer to their creator -- is exclusive to their religion and must not be used by non-Muslims.
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Muslim ethnic Malays make up more than 60 per cent of the diverse country's 28 million people.
Malaysia has sizeable ethnic Chinese, Indian and other communities. About 2.6 million people are Christians.
Church leaders have vowed not to back down.
"Christians in Malaysia have no choice but to use the Malay-language Bibles. To say they cannot use these bibles, it means saying 'you are not allowed to worship in the language that you want'," Rev Hermen Shastri, general secretary of the Council of Churches of Malaysia, told AFP.
The newspaper has launched a long-running court challenge, angering Muslim conservatives, who have demanded Christians use alternative Malay words.
"Why insist? They have an option. They don't really have to use 'Allah' to worship," said Yusri Mohamad, chairman of Muslim rights group Pembela. "This is unnecessary provocation... This is not healthy for Malaysia."
Muslim conservatives have suggested Christians use other Malay words, such as "Tuhan", to refer to God.
But non-Muslims allege growing intolerance by influential Islamic conservatives.