"The operations have been managed well, the suspects were arrested and the weapons seized, so Obama's visit won't be affected," security ministry anti-terror chief Ansyaad Mbai told AFP.
In an update to reporters, police said 16 suspects had been charged under anti-terrorism laws since a major raid late February on an extremist training facility in a remote region of Aceh province in the north of the island of Sumatra.
"Sixteen (suspects) were arrested and three died," national police chief Bambang Hendarso Danuri said.
Two of them were suspected of supplying firearms and were arrested in West Java and the capital Jakarta.
"What's clear is that this has nothing to do with the Free Aceh Movement (GAM). This is purely a group that is preparing something," Danuri said, referring to the former Aceh separatist group which rules the restive province under a 2005 peace-for-autonomy deal.
The hunt for other suspected militants was ongoing, Danuri added.
Police have said three policemen were killed after an intense exchange of gunfire on Thursday.
In the February 22 raid, police found rifles, Malaysian military uniforms and propaganda material including videos of the 2002 bombings on the Indonesian resort island of Bali which killed more than 200 people.
Police have said previously those arrested were "strongly suspected" of being part of regional terror group Jemaah Islamiyah, which has been blamed for multiple attacks across Indonesia.
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