This follows the resignation of Lin Homer in January after four years in post.

The appointment of Thompson as first permanent secretary has also triggered a governance review at HMRC. As a result, the tax authority is looking at governance procedures and the structure of the Board going forward which includes the appointment of a permanent executive chair.

As a result of the governance overhaul, the arrangements for assuring large tax settlements in HMRC will be reviewed. This follows widespread criticism of the recent tax deal with Google which resulted in the settlement of a £300m plus payment.

At the same time, Edward Troup has been promoted to executive chair and first permanent secretary from his current role as tax assurance commissioner and second permanent secretary.

Under the new leadership structure, Troup will chair HMRC’s Board and Jon Thompson will chair HMRC’s executive committee and will be the accounting officer for HMRC.

Thompson, currently permanent secretary at the Ministry of Defence, will join HMRC shortly, after seven years at the MoD. He has a financial background in public sector organisations with previous roles including director general of finance at the MoD, director general, corporate services, at the Department of Children, Schools and Families; finance Director, Ofsted, and director of finance and resources, North Somerset Council.

Troup has been at HMRC in senior roles for a number of years, since he joined the tax authority in 2012 after six years at the Treasury. Prior to moving to the public sector, he was a partner and head of tax strategy at Simmons & Simmons until 2004. He takes up his new role on 5 April.

Cabinet Secretary, Sir Jeremy Heywood, said: ‘Edward’s deep tax expertise and long experience in both HMRC and HM Treasury make him an excellent choice to lead the department through an important phase of change and amid unprecedented public interest in taxation.

‘Jon’s experience of leading one of the biggest departments in government, coupled with his strong financial background, make him strongly placed to deliver HMRC’s ambitious transformation plans, large-scale operations and modern customer services.’

The appointments come at a time of significant reorganisation and change at HMRC as the organisation moves to a purely digital platform over the next five years. Major changes include the rollout of digital tax accounts and abolition of self assessment, plans for a revamped tax agent strategy which is causing concern across the profession, as well as the closure of the majority of small local offices which will be replaced with a number of larger regional hubs, as the HMRC modernises its systems and processes, and provides a fully digitised online service for taxpayers.

Thompson said: ‘While it will be a wrench to leave the Ministry of Defence, I am excited to be taking up the challenge of leading the delivery of the department that raises the revenues that pay for the nation’s public services. With 50 million individual and 5 million business customers, HMRC operates at a scale that few organisations can match.’

The appointments were approved at the highest level and welcomed by the Chancellor George Osborne.

The Chancellor said: ‘These are exceptional appointments to HMRC. We have one of the country’s pre-eminent tax experts and ‎an outstanding civil service leader with experience of transforming large organisations. Edward’s wealth of experience in tax and Jon’s operational and financial expertise, most recently as permanent secretary at the Ministry of Defence, will prove a huge asset to HMRC as it improves its customer service and continues its vital work to clamp down on tax avoidance and evasion.'

Under the new structure, Edward Troup will chair HMRC’s Board and Jon Thompson will chair HMRC’s Executive Committee and will be the Accounting Officer for HMRC.