The Coalition's Cahyo Pamungkas said the move would cause mistrust among the Papuan people and prove counter-productive.
He said it was being done in order to continue exploiting natural resources and controlling the land of Papua.
"This top-down decentralisation which is being done arbitrarily by the central government is like repeating the model of Dutch power in order to continue exploiting natural resources and controlling the land of Papua", said Pamungkas in a statement.
Amnesty International Indonesia Executive Director Usman Hamid said creating new provinces must involve the Papuan People's Council which represents the cultural interests of indigenous Papuans.
Public Virtue Executive Director Miya Irawati said the government must cancel or postpone the move until there is ruling by the Constitutional Court on a challenge against the revisions to the Otsus Law which was launched by the MRP.
According to Irawati, the move by the House of Representatives' Legislative Body (Baleg) and the government in agreeing to the draft law on the creation of three new provinces in Papua is a setback for democracy in Papua.
"We also urge the government to cancel the planned creation of new provinces in Papua or at least postpone the plan until there is a ruling by the MK in several months time", said Irawati.
Under the draft law, South Papua province will be given the name Anim Ha with the provincial capital being Merauke and covering the regencies of Merauke, Mappi, Asmat and Boven Digoel.
Central Papua province will be renamed Meepago with the provincial capital being Timika and covering the regencies of Mimika, Paniai, Dogiyai, Deyiai, Intan Jaya and Puncak.
And Papua Central Highlands province will be named Lapago with the provincial capital being Wamena and covering the regencies of Jayawijaya, Puncak Jaya, Lanny Jaya, Mamberamo Tengah, Nduga, Tolikara, Yahukimo, and Yalimo.
The Humanitarian Coalition for Papua is a voluntary partnership made up of a number of organisations and individuals including Amnesty International Indonesia, the Indonesian Communion of Churches Papua Bureau, and the Democracy Alliance for Papua.