Jon Thompson is set for new role in Whitehall as head of Financial Reporting Council

This article is more than 1 year old

This article is more than 1 year old

The head of HM Revenue and Customs has announced he is stepping down, months after he revealed he had received death threats for warnings over Brexit costs.

Sir Jon Thompson announced he was quitting as chief executive after three years to take on a new role in Whitehall as head of the Financial Reporting Council.

The straight-talking Thompson, who joined in 2016, was highly regarded in the civil service and was not afraid of telling inconvenient truths about the cost of Brexit at his numerous appearances at select committees.

As early as September 2017 he was warning the government about Brexit fantasies, telling a select committee that border and tax checks after Brexit could require an extra 5,000 staff, with new customs checks costing the taxpayer up to £800m.

Last year he revealed he received death threats after disclosing that the post-EU customs option preferred by Brexiters would cost up to £20bn.

His departure is the third blow to the government’s Brexit planning, coming hot on the heels of the retirement of Karen Wheeler, who was in charge of Brexit border delivery at HMRC, and Tom Shinner, 33, who left his job in charge of no-deal planning at the Department for Exiting the European Union for a role in the private sector.

Thompson was also credited with successive, record-breaking increases in the collection of tax revenues, reducing the gap between tax owed and received, and cementing the online business tax returns system with the Making Tax Digital reforms.

He described his time at the helm as “tremendous privilege”, saying: “I’m immensely proud to have led HMRC as we delivered year-on-year increases in the collection of revenues due for public services; prepared for Brexit and the challenges it will bring; and oversaw a recovery in customer service levels making dealing with their tax affairs easier for everyone.”

Sir Mark Sedwill, cabinet secretary and head of the civil service, said: “I am grateful for the enormous contribution Sir Jonathan has made during his time at HMRC.”

In an interview with the civil service trade magazine, Civil Service World, Thompson described his modest background as the son of a man who worked in a newspaper factory all his life and a mum who had mental health problems.

“I went to a comprehensive school, left at 18 and became an apprentice; then 30 years later I was offered the job of permanent secretary of the Ministry of Defence. There is a long journey in those 30 years,” he said.

He went on to run one of the biggest and most critical departments in Whitehall, where insiders say he will be missed.

“He was such an unusual boss. He was an exceptional leader, and was really passionate about gender and reform and motivating people,” said one.