Malay-speaking Christians prayed and sang hymns using the Arabic word, a practice they have observed for hundreds of years but which has sparked an increasingly tense 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 the church.
"(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.
Under pressure from Muslim conservatives, Prime Minister Najib Razak said on Friday that Malaysian Christians must heed rules forbidding them from using the word.
Islamist ethnic Malays say the word is exclusive to Islam and must not be used by the country's non-Muslim minorities. Muslim ethnic Malays make up more than 60 percent of the diverse country's 28 million people.
Malaysia has sizeable ethnic Chinese, Indian and other communities. It has about 2.6 million Christians.
Church leaders have vowed not to back down.
"The 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 government in 2007 ordered a Malaysian Catholic weekly newspaper to cease use of the word, arguing that printing it in Christian literature could confuse Muslims and entice them to convert, which is illegal for Muslims in Malaysia.
"Allah'' also is used by Malay Muslims to refer to the Islamic creator.
The newspaper has launched a long-running court challenge, angering Muslim conservatives.
"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.
Malaysia has avoided overt religious conflict for decades and is generally seen as a moderate Muslim country.
But non-Muslims complain of what they see as growing intolerance by increasingly influential Islamic Malay conservatives.
The Malaysian Catholic church argues that "Allah'' has been used by Christians in the country for hundreds of years and that the word predates the founding of Islam.
Tensions sparked by the issue triggered a spate of attacks in 2010 on places of worship, mostly churches.