The Indonesia office of the International Committee of the Red Cross says the request by Jakarta for it to leave the Papua region is not linked to visits by its officials to separatists in jail.
The foreign ministry in Jakarta says the government is offended both by the ICRC's practice of visiting separatists in prison.
However the ICRC says it's not just in Papua that it visits detainees to ensure they are treated properly.
A spokesperson for ICRC Indonesia, Layla Berlemont, says the closure of their Papua office comes after a recent government request that they reassess and renegotiate the agreement under which the ICRC has operated in Indonesia since 1977.
"We do acknowledge as well that the situation in Indonesia changed profoundly from, for example, 1977 to the present... So this assessment will allow us to bring our proposal before the Indonesian and.. let's see how things will evolve."
Layla Berlemont of the ICRC.