The international airport serving Surabaya, the largest city after the capital Jakarta, and four smaller airports were closed on the eve of the Muslim holiday by the eruption of Mount Raung on the main island of Java.
The airport on the remote, eastern island of Ternate was shut due to ash drifting from erupting Mount Gamalama, the transport ministry said.
Weary travellers expecting to join their families for the final night of the Islamic fasting month instead spent the night in packed airport terminals, with many sleeping on the floor.
Airlines are warning passengers at the reopened terminals to expect significant delays, with dozens of flights backed up until the late afternoon.
Indonesian flag carrier Garuda was due to resume flights to and from Surabaya this afternoon, and had chartered two larger planes to help clear the backlog on its more popular routes.
But flights to the closed airports have been cancelled, with Garuda promising to evaluate the situation as it develops.
AirAsia had already today cancelled or rescheduled half a dozen flights from Surabaya after the ministry had earlier ordered the airport to remain shut.
In recent days, people across the vast archipelago have taken to planes, boats and cars to head to their home towns and villages to celebrate Eid, which marks the end of the fasting month of Ramadan and falls today.
Air traffic is regularly disrupted by volcanic eruptions in Indonesia, which is home to 130 active volcanoes.
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