Authorities in Papua are distributing measles, mumps and rubella vaccines after a deadly outbreak in February.
They are also distributing polio vaccines in response to an outbreak in neighbouring Papua New Guinea.
The Jakarta Post reports 21 out of the 29 regencies and cities in Papua have received the MMR vaccines.
A deadly measles outbreak reportedly killed 72 children in the remote Asmat district between September last year and February.
Meanwhile, the Papua Health Agency has distributed polio vaccines to 26 regencies, including the five that share a border with PNG.
A polio outbreak was confirmed in PNG's Morobe province last month, 18 years after the country was declared polio-free.
An official from the Papua Health Agency said several remote regencies have low vaccination rates and local leaders need to do more to raise awareness.