"We ordered the closure of three regional airports ... where visibility was only about 100 metres," Hatta Radjasa, the transport minister, said.
Flight cancellations and delays have also been reported at other airports on Borneo and Sumatra islands, officials said.
The closures threaten to cause travel chaos as millions of people prepare to travel at the end of the Muslim holy month of Ramadan.
At Sultan Thaha Airport in Sumatra’s Jambi province all flights have been cancelled.
"Our airport has been paralysed. No planes are able to land or take off because of poor visibility," Basuki Mardianto, the airport head, said.
About 14.5 million people are expected to travel by road, air and sea from major cities to visit their families in rural villages. Traffic is expected to peak at the weekend.
Rachmat Witoelar, the environment minister, said he was worried that the haze, which is hanging over much of South East Asia, may be prolonged by the late arrival of the wet season. Indonesia's rainy season usually starts in late October but has so far failed to arrive.
The haze has caused Singapore
to issue a health warning
Jakarta has appealed for funds and equipment from its neighbours, Singapore and Malaysia, to combat the smog which is coming mainly from the Indonesian provinces on Sumatra and Borneo islands.
The army has been enlisted to help fight the fires and the government has tried using firefighting airplanes and cloud seeding to extinguish the blazes.
Brush fires are started by farmers or agricultural companies looking for a cheap way to clear land for plantations, often for producing palm oil or timber.
In Malaysia, air quality in the capital Kuala Lumpur has fallen to unhealthy levels leading the government to advise citizens against outdoor activities.
A meeting of leaders from five South East Asian countries last week urged the government in Jakarta to ratify a regional treaty on cross-border haze, and said financial assistance would be withheld until it did.
The smog, which has triggered health warnings in Singapore and Malaysia this year, has plagued the region since the 1990s.