A lawyer for the sect, Haris Mohamad Ibrahim, said that about 30 armed men dressed in Arab robes had attacked the commune with Molotov cocktails.
No-one was injured in the attack, which caused a small fire.
“The roof of the teapot structure is… slightly charred, but since it is made of concrete, the damage is not extensive,” firefighter Ahmad Fakarudin told Reuters news agency.
The sect – based in the strongly Muslim state of Terengganu – claims to promote harmony between religious groups.
Its leader, Ayah Pin, says he is the saviour of the world.
He has attracted believers from many different religious groups with his message of love and tolerance. He claims to allow his followers to be members of any faith, including Islam.
Earlier this month, the group was raided by police, and 21 followers were arrested for possessing documents contrary to Islam. They were all freed on bail pending a court appearance in September.
Members have been jailed in the past for attempting to renounce Islam, and the group’s bizarre constructions have been deemed to be against local regulations.
The group’s controversial structures are said to combine architectural elements from Islam, Christianity, Hinduism and Buddhism.