The petition, presented by the independence leader Benny Wenda on Tuesday, asked the UN to appoint a special representative to investigate abuses and to put West Papua back on the decolonisation agenda.
But the UN decolonisation committee says the West Papua cause is outside its mandate, which extends only to the 17 states identified by the UN as "non-self governing territories."
The committee's chair and Venezuela's representative to the UN, Rafael Ramírez, says he had received no formal petition document, and his office had been "manipulated" for political purposes.
Mr Ramírez also says the committee accepts Indonesia's sovereignty over West Papua, which took control of the western half of New Guinea in 1969.
RNZI reports in a statement, Indonesia's UN representative, Triansyah Djani, who sits on the committee, called Mr Wenda's petition a hoax and separatist propaganda.