The 33 people were arrested by the police anti-terror unit following last month's attacks in Jakarta which killed four civilians and four assailants, Badrodin Haiti said.
The gun and suicide bomb attacks claimed by the Islamic State group and centred around a Starbucks outlet were the country's worst terror incident in seven years, ending a long lull in major terror.
Police have launched a crackdown across the country, saying they suspect a broader extremist network helped carry out the assault.
A group led by an extremist called Hendro Fernando had received 1.3 billion rupiah (USD 97,000) from Jordan, Iraq and Turkey, he said, adding that it planned to launch attacks against Jakarta's main airport and the national police headquarters.
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Haiti said another group led by a person identified only as 'Helmi' planned to use a car bomb to attack the Jakarta police complex in the city's main business district.
A third group, according to the police chief, planned stabbing attacks on traffic police.
Bahrun Naim is one of three high-profile Indonesians fighting for the Islamic State group in Syria. Police say he played a central role in motivating groups in Indonesia to launch attacks in the country.
"(Naim) explained and gave motivation about launching a holy war and explained how to make bombs and said that he would send money to anyone who is ready to engage in terrorist acts," Haiti said.
Indonesia, the world's most populous Muslim-majority country, suffered several major bomb attacks by Islamic radicals between 2000 and 2009, including the 2002 Bali bombings that killed 202 people.
Police now say the biggest threat comes from two main sources -- Indonesians in Syria encouraging local groups to launch attacks, and Indonesians who return home from fighting in the Middle East.
There are currently 392 Indonesians fighting for IS in Syria and over 50 more are thought to be preparing to leave for the country, police said.