The man had been exposed to IS ideology while serving a five-year jail term in Indonesia. He was involved in a plot to kill high-profile individuals and attack Christian, Hindu and Buddhist places of worship and entertainment outlets around Kuala Lumpur, the police chief added.
The two other suspects, Muhammad Syazani Mahzan and Muhamad Nuurul Amin Azizan from Malaysia, were arrested on May 14 in the northern Malaysian state of Kedah, police said.
The Malaysian police chief said these two suspects had undergone bomb-making training in the Indonesian city of Yogyakarta in 2018 which was conducted by the terror group Jemaah Ansharut Daulah. They had been seen surveying several churches in Yogyakarta to launch attacks.
The suspects are thought to have links to a wider IS-inspired cell, some of whose members were detained last week in Malaysia.
Malaysia and Indonesia, both Muslim-majority countries, are on high alert amid fears that IS supporters are plotting attacks after the group's defeat in the Middle East.