The alleged seizure of the Bibles, imported from neighboring Indonesia, is certain to reignite complaints by religious minorities that their right to practice their faiths freely has come under threat as the government panders to the Muslim majority.
A growing sense of discrimination among the minorities is chipping away at Malaysia's reputation as a harmonious multiethnic nation that practices a moderate brand of Islam.
The Rev. Hermen Shastri, general secretary of the Council of Churches of Malaysia, said authorities seized a consignment of 10,000 copies sent from Jakarta to Kuching in Sarawak state on Sept. 11 because the Indonesian-language Bibles contained the word "Allah."
Indonesian language is similar to Malaysian language, both of which use "Allah" as translation for God in both Islamic and Christian traditions.
Another 5,100 Bibles, also imported from Indonesia, were seized in March, said an official from the Bible Society of Malaysia, who asked not to be named for fear of angering the government.
A Home Ministry official said he was not aware of the seizures. He said he couldn't be named without his superiors' clearance.
Malaysia has banned non-Muslims from using the word "Allah" in their texts, saying the word is Islamic and may upset Muslims.
About 60 percent of the country's 28 million people are Malay Muslims while 25 percent are ethnic Chinese and 8 percent are Indians. Many of the Chinese and Indians are Christians.
The Roman Catholic Church is challenging the "Allah" ban in court, saying it is unconstitutional and discriminates against those worshipping in Malay language. The case has been stuck in preliminary hearings for almost two years.
Shastri said the church council is concerned over the continued detention "of our holy book, which is depriving congregations ... and denying them the use of their Bible."
"For most of the Christians, this is not an issue of going against the authorities. They have been using (the word "Allah") for a long time," he said.
Church officials say Allah is not exclusive to Islam but is an Arabic word that predates Islam.
Besides the Bible seizures, Malaysia has been embroiled in other religious disputes. Some were over the conversion of minors to Islam and the religion of deceased people who are said to have converted to Islam secretly before their death. Hindus have also protested the demolition of several temples by authorities.