The MI2 helicopter went down mid-morning after it hit poor weather in south central Bago, according to the statement released by the office of the army's commander-in-chief.
It was flying south from Meiktila to an air base near Yangon, the former capital and largest city.
"All three crew members... Who were on board died on the spot," the statement said.
"Authorities plan to investigate the cause of helicopter crash," it added.
Myanmar has a busy aviation sector, partly to compensate for the country's poor road and rail infrastructure.
In February, all five crew died when a Myanmar air force plane crashed in the capital Naypyidaw soon after take-off.
Last year an Air Bagan ATR 72 twin-engine turboprop carrying 49 passengers skidded off the runway after landing during heavy rain at Yangon International Airport.
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