Picture used for illustrative purposes only.
The helicopter went down near Khost, a small town in Balochistan province bordering Afghanistan and Iran.
"A helicopter on a flying mission crashed late last night. Six personnel — including two army majors (both pilots) embraced shahadat (martyrdom) in the crash," the military said in a statement.
No further details were given about the cause of the crash or type of aircraft. The area where the helicopter came down has not been hit by recent flooding.
In early August, six Pakistan servicemen including one of the army's top commanders were killed when their helicopter crashed during flood relief operations in Balochistan.
Fierce monsoon rains have caused devastating flooding in Pakistan this year — particularly in Sindh and Balochistan provinces.
More than 1,600 people have died, 323 in Balochistan.
The bodies of the three occupants were found at about 1.30am (0030 GMT), an interior ministry statement said. France's Mediterranean coast has been hit by heavy rain over the last week that has led to serious flooding and widespread transport disruption.
There were no casualties on the ground or damage to property, according to an air force statement. Pakistan's President Afif Alvi expressed his condolences to the family of the pilot, Noman Akram.
The bodies had not been found as of Friday afternoon, according to the official. Representatives of the Federal Aviation Administration and the National Transportation Safety Board were traveling to the area to investigate.
An official described seeing one child with part of his leg missing lying on the hospital floor for several hours, without receiving treatment for lack of medical staff.
The Ruler of Sharjah was briefed on the project, which comes within the framework of developing the electricity production sector system and is SEWGA largest investment in the field of energy in the emirate.
After repeated setbacks in the operation, military engineers and skilled miners are working by hand in a painstaking dig through rock and rubble towards the men using a so-called "rat-hole" mining technique to clear the final stretch.