Thousands of people in Pekanbaru of Riau province in Sumatra held Islamic prayers for rain outside the governor's office. Many of those taking part wore face masks to protect themselves from the smoke.
Similar prayers were held in towns in Kalimantan on Borneo island, where air quality has been at unhealthy levels and schools forced to close.
Fires have burnt through parts of Sumatra and Borneo islands for more than a month and the Indonesian government has sent 9,000 military, police and disaster agency personnel to fight the flames.
Indonesian authorities are using 37 helicopters and 239 million litres of water bombs to attack the blazes, while aircraft were seeding clouds in the hope of generating rain.
The country’s disaster agency said 5,062 fire "hot spots" had been detected in six Indonesian provinces, as of September 11 morning.
Endro Wibowo, deputy police chief of the town of Sampit in Central Kalimantan province, said his team was working around the clock to put out the fires.
Indonesia has been facing a severe dry season induced by El Nino that triggered drought and forest fires in several provinces this year. Wildfires occur in Indonesia in every dry season due to traditional burning practices in agriculture to clear land for palm oil and pulp plantations.