A heavy haze triggered by the fires forced the postponement of the first exercise, Bernama reported Tuesday.
Military doctors handed out face masks and instructed all pilots and officers to give priority to aviation safety.
The exercises are taking place at Pekanbaru air base on Sumatra Island.
Indonesian President Susilo Bambang Yudhoyono has apologized for the forest fires that blanketed parts of Singapore and Malaysia.
He pledged to step up his country's efforts to tackle the problem as air pollution levels worsened near Malaysia's largest city, Kuala Lumpur, The Wall Street Journal reported.
Officials and activists blame the acrid haze on slash-and-burn farming techniques to clear land for palm oil plantations and other agricultural developments.