“A substantial operational failure” in the department of Revenue and Customs has led to the departure of its chairman, Paul Gray.

His resignation came as the Chancellor admitted that discs containing the personal records, including bank details, of up to 15 million child benefit claimants had been lost in transit to the National Audit Office, the government’s own financial watchdog.

Gray admitted in his resignation letter that HMRC still faced “some major issues where we need to do better” but made no explicit reference to HMRC’s recent failures in protecting personal data.

Earlier this month HMRC admitted that it had lost a CD containing 15,000 names, national insurance numbers and dates of birth of thousands of holders of Standard Life pensions. The data was “lost in transit by HMRC’s external courier”, the agency said.