Deputy Security Minister Mohamad Johari Baharum told AFP that The Herald should comply with the government order.
"We approved the permit. Now the weekly should comply with the government decision not to use the word Allah," he said.
Authorities on Sunday allowed The Herald to continue to print, after earlier threatening to revoke its license in a row over its use of the word "Allah."
The publishers then assumed that they could use the word Allah, or God, which is used by church leaders when they deliver sermons in Malay or in the Malay language articles section of the 28-page newspaper.
Editor Father Lawrence Andrew told AFP Friday that the paper would still press ahead with its lawsuit filed last month to challenge the state order banning it from using the word Allah.
"We will not withdraw the lawsuit," he said.
Andrew also said that the newspaper used the word Allah in its first issue for 2008 dated January 6.
Abdullah Mohamad Zain, minister in the prime minister's department said the Cabinet at its meetings on October 18 and November 1 decided that the word Allah could only be used by Muslims to avoid confusion.
Abdullah said non-Muslims should use the word God ("Tuhan" in Malay) instead, although the word Allah has been used in the Malay-language Bible for centuries.
"The use of the word Allah by other religions may arouse sensitivity and create confusion among Muslims," he was quoted as saying by the Star newspaper Friday.
Malaysian commentators have sounded alarm over the growing "Islamization" of the country and the increasing polarization of the three main ethnic communities, which mix much less than in the past.
In recent weeks there have been controversies over the construction of the world's tallest Taoist Goddess of the Sea statue on Borneo island and destruction of Hindu temples by local authorities.
Religion and language are sensitive issues in multiracial Malaysia, which experienced deadly race riots in 1969.
The Herald, a tabloid-sized newspaper, is circulated among the country's 850,000 Catholics with articles written in English, Chinese, Tamil and Malay.
About 60 percent of the nation's 27 million people are ethnic Malay Muslims who dominate the country's politics. The rest are mostly Buddhist, Hindu or Christian Chinese and Indians.
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