Speaking to the AFP news agency, Raja Petra's wife, Marina Lee Abdullah, said he had been detained for allegedly "insulting Islam and publishing articles on his website which has tarnished the country's leadership to the point of causing confusion among the people".
His lawyer, Malik Imtiaz Sarwar, said his client had also been held for allegedly inciting racial tensions with his writings.
"He was taken this morning to Kamunting (Detention Centre)," Malik said.
"This is definitely a big blow to the idea of civil liberties, especially in a climate when everybody is asking for greater rights."
|Raja Petras has been a frequent critic of the government [EPA]
Raja Petra's detention comes amid escalating political tensions in Malaysia, with the government's popularity at an all time low after suffering its worst ever result in March general elections.
The opposition, led by former deputy prime minister Anwar Ibrahim, has said it plans to oust the current leadership by orchestrating the defection of more than 30 government MPs.
Malik said he intended to ask the High Court in Kuala Lumpur to rule on whether Raja Petra's detention is legal.
However, under Malaysian law the country's home minister has the final word on how long a person can be held under the ISA.
The courts can only review the procedure of the detention, not the detention itself.
Raja Petra was arrested on September 12, triggering protests from opposition supporters demanding his release and calling for the ISA to be abolished.
An opposition MP and a Chinese Malaysian journalist were also arrested under the ISA on the same day but they were both subsequently released.