The flight from Abu Dhabi was about 45 minutes away from Jakarta on Wednesday when the turbulence hit.
The plane, an Airbus A330-200, landed safely after the incident, but nine people were taken to hospital.
The United Arab Emirates' national airline said the cabin luggage bins were damaged and passengers said oxygen masks were released during the shaking.
In a statement, the airline said 22 people had been "treated by paramedics for minor injuries at the airport. Nine other passengers have been taken to a local hospital".
Indonesian transport ministry spokesman Hemi Pamuraharjo said at least eight Indonesian passengers and a foreign flight attendant were hurt, with several suffering broken bones, the Associated Press news agency reports.
A number of those on board were Muslim pilgrims returning from Saudi Arabia. "It happened when I was performing prayer," passenger Nenden Nurhaini told the Jakarta-based news website Okezone. "The plane suddenly began to shake so fast."
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