New members of the Papuan People's Assembly, the MRP, have been urged by Indonesia's government to stay away from politics.
The Home Minister Gamawan Fauzi told new MRP members to instead focus on protecting the rights of indigenous Papuans as he addressed them at their inauguration ceremony in Jayapura.
The Jakarta Post reports that all but two of the 75 elected MRP members from Papua region were inaugurated.
One of those missing was Agus Alue Alua, the chairman for the MRP's first term who died last week.
However he was controversially omitted from the inauguration line-up before his sudden death.
Some Papuan commentators claim the Papua leader was sidelined by Jakarta because of his role last year's mass demonstrations rejecting special autonomy.
The inauguration was held under tight security, with nearly 800 police present, after rumours that rallies would be conducted by groups opposing special autonomy.