Herald newspaper editor Father Lawrence Andrew said the move was part of a series of restrictions put in place by the conservative Muslim government when it renewed the paper's licence on Tuesday.
The Herald, circulated among the country's 850,000 Catholics, nearly lost its publishing licence last year for using the word "Allah" as a translation for "God," with authorities saying it should only be used by Muslims.
"The Constitution says Malay is the national language so why can't we use the national language in Malaysia?" he told AFP.
He called the ban "unacceptable" and said he intended to take action.
Andrew said the ban did not make any sense because a large proportion of Catholics in Malaysia are Bumiputera who mainly speak Malay.
The term "Bumiputera", or "Son of the soil", refers to ethnic Muslim Malays and the indigenous inhabitants in peninsular Malaysia and on Borneo island who are mostly Christian.
"More than 50 percent of our congregation are Bumiputera and two of our bishops are Bumiputera," he added.
The issue will be decided by the courts next month, while home ministry officials told the New Straits Times daily Thursday they will be monitoring the paper's actions closely.
Religion and language are sensitive issues in multiracial Malaysia, which experienced deadly race riots in 1969.
About 60 percent of the nation's 27 million people are ethnic Malay Muslims, who dominate the government. The rest of the population are mostly ethnic Chinese and Indians -- practising Buddhism, Christianity and Hinduism.
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(Source: AP)