Zaw Dias, Pangkalan Bun and Hani Cai were arrested before boarding the airplane to China.
The two were facing five charges, including sedition, espionage and violating Indonesia’s Prevention of Counterfeiting Act.
The two are members of groups known as the United Malays National Organization — also known the MBN-PON — a group that has called for a split with the government.
They are also accused of being involved in the 2014 bombing of a bar and restaurant near the Indonesian consulate in Kuala Lumpur which killed six people and wounded more than 50 other.
The Indonesian public prosecutor’s office ordered that the pair remain in custody for 45 days.
Indonesian President Joko Widodo has refused to interfere in a case involving ethnic Malays, including a prominent Ulema cleric.
The Ulema were upset after the ruling party-backed government in May called on the government to crack down on anti-Malaysian extremists.
The government also claimed the group does not speak a Malay language “because we are Malay.”
The religious and political leaders have accused the government of using the Ulema as a tool to keep the country “Malay” for political gain.
The government has since been pressuring the community to come to terms with their past, to be seen as a nation of peace but also a nation of Muslims.
Malaysia’s Ulema have been accused of being among the most militant members of Malaysia’s homegrown Islamist Islamist terrorism movement, including the Islamic State (IS) and al-Qaeda.