An international health NGO says the death toll from a cholera epidemic in Indonesia's Papua has reached an estimated 200.

Medecins du Monde says it has recorded 150 deaths from cholera in the Dogiyai and Paniai districts of Papua since April but estimates the actual toll could be towards the figure of 290 which local church groups are reporting.

The NGO's medical coordinator, Dr Remco van de Pas, says from their work on the ground in the remote area, around 800 current cases of cholera have been seen although the outbreak is tailing off.

"But it's basically the tip of the iceberg of several health problems and access to clean water and access to education that you see. I believe that this cholera bacterium is always there. When people are in a lower nutritional state, or they have another disease like HIV/AIDS, then they are more vulnerable to this and this is the case in this area."

Dr van de Pas says the government responded by sending medical teams although they have arrived late and in many cases haven't reached affected villages.