Agung Prabowo, 23, was accused of helping to create a website that suggested ways to assassinate foreigners in the capital, Jakarta, said Colonel Petrus Reinhard Golose of Indonesia's anti-terror task force, on Wednesday.
The other suspect, Agung Seyadi, 31, allegedly bought a computer for a jailed Bali bomber, Imam Samudra, who planned to use it to collect funds for terrorist attacks, he said.
The men were arrested this month, Golose said, but neither has been formally charged.
Attacks in Indonesia have been blamed on regional terror group Jemaah Islamiyah since the bombings on the resort island of Bali that killed 202 people, many of them foreign tourists.
Attacks in Jakarta in 2003 and 2004 took at least 21 lives and suicide attacks in Bali last year caused 20 more deaths.
Late last year, authorities discovered a website that outlined the best way to assassinate foreigners in Jakarta, providing tips as to where they could be found and instructions such as "ensure the target is killed by shooting him several times in the heart and head".
Samudra, who is awaiting a death sentence on charges of planning and carrying out the 2002 Bali attacks, wrote a book in jail, one chapter of which discussed credit card fraud over the internet as a way to fund terror attacks.