About 30 people armed with knives, sticks and plastic bags with flammable material attacked the Sky Kingdom commune in the northeastern state of Terengganu before dawn on Monday, the Star newspaper said on its website.
No injuries were reported.
Police in Terengganu declined to give details of the attack, but state official Mohamad Ramli Nuh confirmed that there was a rampage by an "unidentified group of people".
"We believe these people are ordinary members of the public who are so angry with the deviationist teachings of Ayah Pin that they decided to take matters into their own hands. The security situation is now under control," he said.
The sect's leader, 65-year-old Ariffin Mohammed, also known as Ayah Pin, left the area earlier in the night, and his whereabouts were not known, the Star reported.
The Sky Kingdom sect says it has followers from all religions and races in Malaysia, and denies it is spreading deviant teachings.
The group drew attention this year after constructing a house-sized teapot, umbrella and boat within the commune, describing them as structures of interfaith harmony.
Arsonists set fire to the teapot, umbrella as well as several other buildings and at least one vehicle, witness Shahrom Bakar said.
"The windows to some buildings and homes were also smashed but I did not see anyone injured," said Shahrom, a cameraman for a local TV network.
"We believe these people are ordinary members of the public who are so angry with the deviationist teachings of Ayah Pin that they decided to take matters into their own hands. The security situation is now under control"
Mohamad Ramli Nuh,
Terengganu state official
The Star quoted an unidentified follower of the sect as saying the attackers damaged buildings and four vehicles but did not injure anyone.
"They smashed our house windows but the people were not harmed," the sect member said. "They told us not to get involved and we didn't want to confront them."
Religious officials and police raided the commune early this month and arrested 21 followers who were charged under an Islamic law that makes it illegal to posses documents contrary to the religion in predominantly Muslim Malaysia.
All 21 were released on bail, and their trial begins on 23 September.