The incident, which occurred during a routine landing at a "tactical landing zone", described by the spokesman as something less permanent than an airstrip, resulted in "minor injuries" to two passengers.
The MoD said in a statement that all 38 people on board, including the two injured, had been able to escape to safety.
The ministry said that another reason for destroying the aircraft was to prevent insurgents from being able to "obtain information on specialist equipment" on board.
"The site was secured and after a thorough assessment of the damage it was concluded that the aircraft could not be recovered without exposing our personnel to undue risk," the statement said.
The statement said the plane was "safely destroyed".
An MoD source said that explosives experts placed charges in the aircraft and set them off in a controlled explosion.