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Administrators were reported to have "inconsistently interpreted" the policy over a period of "many years", with some confusion over the system arising as far back as 2002.
A June 2014 letter to MoD officials also said the Army was "firmly of the view" the debts should be written off due to "compelling" operational reasons.
The Army said a decision to recover the pay must be considered against the "significant risks" that losing experienced air crew and senior instructors "would cause to air safety and the longer term costs of training replacements".
It took four years to train an attack helicopter pilot at a cost of £3.5m, with the cost of training an instructor put at £8.5m.
It was said that 15 pilots were "directly citing the incorrect payment as the deciding factor in their decision to leave the Army".
The issue has also "been identified as a factor in the decision to leave" in other resignations.
The Army said it was not aware of any resignations linked to the overpayments since 2014.
A spokeswoman said: "We have apologised and explained the circumstances of the overpayments to all of those affected.
"In accordance with standard government practice, arrangements have been made to revert their pay to the correct levels and all affected personnel are now receiving the correct pay."