This leaves the tax authority with vacancies in two of the most senior roles at HMRC as it enters a major digitisation programme with the rollout of the Making Tax Digital quarterly reporting system. The departure of Ruth Owen, director general of customer service, was announced on 4 April. It is also only a year since Lin Homer resigned from HMRC to be replaced by Jon Thompson as HMRC chief executive.

Granger will leave HMRC at the end of May. Details of any interim appointments will be announced in due course, HMRC said.

She joined HMRC in October 2012 from the Australian Taxation Office (ATO), where she worked as a commissioner law, responsible for a range of ATO expert areas; including the ATO’s law practice responsible for interpretation of the tax and superannuation laws, and the government and Treasury relationships, including ATO input into design and implementation of new laws.

Under Granger’s leadership, HMRC has transformed its compliance activities, introducing controversial compliance initiatives such as direct recovery of debt (DRD) and accelerated payment notices (APNs).

It has also ramped up its activity on facilitators and enablers to clamp down on tax evasion. HMRC said that ‘this has all helped support the department’s transition to a “promote, prevent, respond” approach to compliance across the UK.

One of the major planks of the compliance activity was assumed to be Making Tax Digital, which is supposed to raise an additional £280m in tax revenues a year by targeting those who HMRC believes make mistakes on their tax returns or fail to comply at all.

At the same time, the amount of revenue collected through HMRC’s compliance work has increased, rising to £26.6bn last year. The department has also recruited 12,000 people into compliance, although HMRC is also going through a major transformation programme with office closures across the country with a move to a dozen or so regional hubs.

Just a day after the news that  Owen was leaving, the tax authority will need to focus on a very effective succession programme to ensure that these senior roles are filled quickly.

Granger said: ‘Leaving HMRC will be really difficult. I can honestly say that this has been one of the best and most rewarding roles that I’ve ever had. I’ve enjoyed my time here so much that I actually stayed here far longer than I originally planned to.

‘It’s been an absolute privilege to have been part of team HMRC at such a pivotal time. Now that the customer compliance group is firmly established it feels like the right moment to hand over to a new leader. It’s also time for a little bit of rebalancing for me personally. So while I’ll be sad to go, it’s definitely the right time, both for me and for HMRC.’

HMRC chief executive Jon Thompson said: ‘It’s been great working with Jennie over the last year, and her enthusiasm for HMRC and her commitment to her teams will be hard to replace. She’s made an enormous contribution to the work of the department and I know she’ll be sorely missed.’

During her time at HMRC, Granger was also a Commissioner for HMRC and a member of the Executive Committee, as well as the organisation’s diversity champion for race.