At least four people have been killed in the political violence following protests over perceived racial and ethnic discrimination, spread over two weeks in a string of Papuan towns.
Some protesters have demanded a referendum on independence, something the government has ruled out. Papua and West Papua provinces, the resource-rich western part of the island of New Guinea, were formerly a Dutch colony that was incorporated into Indonesia after a widely criticized U.N.-backed referendum in 1969.
National police spokesman Dedi Prasetyo told journalists late on Monday that separatist leader Benny Wenda, who has political asylum in Britain, had provided funding for his network of supporters, and instructed them to organize mass gatherings and prepare weapons.
"The riots in Papua were by design," Prasetyo said, adding that Wenda's United Liberation Movement for West Papua (ULMWP) was trying to force the issue onto the agenda of the current sessions of the United Nations Human Rights Council.
Giving the update on the number of people arrested, Prasetyo did not specify what charges they faced, but he said two of the suspects were "the intellectual actors" who "designed the riots." He said police were still hunting 20 more suspects.
Speaking to Reuters by telephone, Wenda denied orchestrating the protests, and demanded that the government explain the heavy-handed response of security forces to the "peaceful demonstrations."
Wenda's ULMWP issued a report on Monday saying more than 200,000 Papuans took part in the protests, which saw the unfurling of "Morning Star" flags - a banned separatist symbol - at several government offices. The report also accused security forces of causing the death of 11 civilians.
Police spokesman Prasetyo said only three civilians and one military personnel died, most of them as a result of being struck by arrows. In Papua, the traditional bow and arrow is still used for hunting and as a weapon.
Accusing the Indonesian military of "killing my people," Wenda urged the United Nations to discuss Papua at its meetings in New York and asked Indonesia to allow U.N. officials to visit Papua.
Indonesian officials have said that foreigners are currently barred from visiting Papua for security reasons.
In Jakarta, President Joko Widodo met with Papuan leaders and students at the presidential palace on Tuesday in a bid to soothe tensions. He offered employment at state firms for Papuan college graduates and more development in a region that has the highest poverty levels nationally.
The latest protests followed racist slurs against Papuan students, whose dormitory was tear-gassed during their detention in the city of Surabaya on Java island on Aug. 17, Indonesia's Independence Day, for allegedly desecrating a national flag.An internet blackout had been lifted for most parts of Papua after three weeks, though it remained in place for major cities like Jayapura, Manokwari and Sorong.