A Malaysian church group accused the government on Monday of harassing Christians after customs officers seized 32 Bibles from an airline passenger.

The Council of Churches of Malaysia said the officers at a Kuala Lumpur airport had on January 28 confiscated the Bibles from a Malaysian Christian woman who was returning home from Manila.

"The Council of Churches is flabbergasted that such acts are happening in our country with such frequency and impunity," its General Secretary, Rev Hermen Shastri, said in a statement.

"We call upon the prime minister...to make a clear and unequivocal statement to assure Christians in the country that they will not be subject to such harassment," he said.

The Bible seizure is the latest in a series of disputes that is stoking fears of an erosion of non-Muslims' rights.

The reverend said the Internal Security Ministry, which vetted the Bibles, should immediately release them.

A senior ministry official, who declined to be identified, said the matter had been resolved and the Bibles would be immediately returned to the owner.

"The books should not have been confiscated in the first place," the official said by telephone, adding that they were not on the banned list.

Last month, the government decreed that a Catholic newspaper cannot use the word Allah, upholding a ruling that non-Muslims are forbidden from using the word to describe their God.

Politically dominant Malay Muslims form about 60 per cent of the population of about 26 million, while the ethnic Chinese and Indian minorities include Hindus, Buddhists, Christians and Sikhs.