The British army has lost some of its most experienced helicopter pilots over a wage error that led the Ministry of Defence to demand they returned thousands of pounds in overpayments, according to newly released documents.

Defence chiefs were urged to drop their bid to recover the wages after 15 attack helicopter pilots resigned over the issue, in which servicemen faced paying back a total of £829,000.

The army raised concerns that the loss of experienced pilots and instructors risked not only undermining morale, but had the potential to threaten the Apache attack helicopter squad’s frontline capabilities in Afghanistan.

About 200 attack helicopter pilots and instructors, a quarter of who are now retired, received overpayments of up to £30,000 each and faced action to recover the money despite officials accepting it was taken in good faith.

Despite concerns over the impact of attempting to recover the debt, the process to recoup the overpayments has continued.

A letter to MoD officials in June 2014 said the army was “firmly of the view” that the debts were written off due to compelling operational reasons, including the fact that the cost of replacing just one pilot far exceeded the total debt.

It warned that there had been an increase in the number of pilots leaving since debts were placed on their accounts, “with 15 pilots directly citing the incorrect payment as the deciding factor in their decision to leave the army”.

At the time the document was written it took four years to train an attack helicopter pilot at a cost of £3.5m. The cost of training an instructor was £8.5m.

The army said a decision to recover the pay had to be considered against the significant risks losing experienced air crew and senior instructors “would cause to air safety and the longer term costs of training replacements”.

It also warned: “The loss of one more Apache qualified helicopter instructor from the operational training pipeline will reduce the trained pilot output to below the level required to maintain frontline crewing ratios.”

Senior army figures were also concerned they could lose their best and brightest pilots and instructors to the commercial sector.

The rules that governed how pilots’ pay was calculated were branded “complicated and contradictory” in the documents released under the Freedom of Information Act.

They added that administrators had “inconsistently interpreted” the policy over a period of many years, with confusion over the system voiced as far back as 2002.

An army spokeswoman said the process to recover the overpayments was continuing and each pilot’s debt was being considered on a case-by-case basis. She said she was not aware of any resignations linked to the debt occurring since 2014.

She 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.

“The overpayment of salary has resulted in an amount of debt owed by individual personnel.”