As many as 15,000 staff have resigned from HM Revenue and Customs since the merger in 2005 - some 3,000 ahead of the management board’s target.

Dave Hartnett, permanent secretary for tax at HMRC, was forced to explain the departures at a recent House of Commons discussion, but said he was not aware of any forced redundancies.

‘There have been no compulsory redundancies that I’m aware of in the last few years,’ he said.

The resignations equate to £663m in efficiency savings.

While a reduction in headcount has been circulating on HMRC’s agenda since the merger, total operating costs are up by £192m, the department has admitted.

Jim Cousins, Labour MP for Newcastle upon Tyne Central, said he could not understand why a decrease in staff numbers coincided with an increase in operating costs.

The technical failures of the eFiling system earlier this year would have added significantly to costs, Cousins said.

Hartnett argued there were ‘any number of reasons’ for the cost problems ‘to do with the running costs of IT systems and child benefits’.

Members of HMRC’s senior management were also forced to defend changes to its own structure.

Mike Clasper, chairman of HMRC, outlined his role, that of Hartnett and newly appointed chief executive officer Lesley Strathie.

‘I have three tasks. To develop the long-term strategy, act as the person who is held to account and ensure the highest standard of corporate governance.

‘Lesley Strathie has the day-to-day accounting role and Dave Hartnett ensures the quality of the tax policy and that the legislation around that is of the highest standard. He’s also responsible for our relationship with the Treasury,’ he said.

Strathie was not present at the Commons discussion.

Clasper’s clarification follows a report released by Kieran Poynter, ex-chairman of PricewaterhouseCoopers, which investigated inadequate data security as highlighted in the loss of 25 million records last year.

Poynter concluded the loss was ‘entirely avoidable’ and made the assertion the incident showed ‘serious institutional deficiencies at HMRC.’