The Papuan separatist group, the West Papua National Committee (KNPB), says its leader Paul Horis has been killed.
The chairman of the KNPB, Victor Yeimo, said MR Horis was killed by Indonesian special forces at the weekend.
Another KNPB member was seriously wounded in the attack.
Mr Yeimo also alleged that a regional member of parliament, Peter Katem, was beaten and tortured by the Indonesian military in the eastern town of Merauke.
Dr Camellia Webb-Gannon, co-ordinator of the West Papua Project at the University of Sydney, told Radio Australia that the reported incidents suggest the Indonesian military is taking "an increasingly hardline and violent approach to the conflict in West Papua".
"This is despite contradictory statements from top political leadership in Indonesia that a development or dialogue approach will be taken," she said.
Several members of the KNPB were arrested recently for making or storing bombs.However, the KNPB insists it is committed to a peaceful campaign for self-determination