Syed Ahmed Alkaff, a 45-year-old Singaporean with Malaysian permanent residency status, was arrested on August 11 at Tanjung Sutera Resort in southern Johor state under Section 295 of the Penal Code for injuring or defiling a place of worship.
He had allowed a group of Buddhists from Singapore to use the prayer hall for chanting. Alkaff was later released on bail.
Home Minister Ahmad Zahid Hamidi said his office had decided to revoke the man's permanent residency status with immediate effect as he did not respect religious sensitivity.
Malaysia, a Muslim majority country, has large non-Muslim ethnic Chinese and Indian communities.