Bible Society officials told Reuters that two of their members were briefly detained following the seizure.
A court ruled in October that non-Muslims could not use the word Allah to refer to God.
The appeals court said the term Allah must be exclusive to Islam or it could cause public disorder.
People of all faiths use the word Allah in Malay to refer to their gods.
Christians argue they have used the word, which entered Malay from Arabic, to refer to their God for centuries and that the ruling violates their rights.
The October court ruling overturned a 2009 ruling which said that a Catholic newspaper, The Herald, could use the word Allah in its Malay-language edition to describe the Christian God.
The 2009 ruling sparked tensions, with churches and mosques attacked.