Department for Transport

Rutnam became Permanent Secretary at the Department for Transport in April 2012^[10] with the Secretary of State, Justine Greening, commenting that his "outstanding record and business focused skillset will be tremendous assets".^[12] As of 2015, Rutnam was paid a salary of between £170,000 and £174,999, making him one of the 328 most highly paid people in the British public sector at that time.^[13]

He oversaw the development of HS2,^[14] the creation of Highways England,^[15] a review of airport policy,^[16] a substantial completion of works on Thameslink,^[17] a new approach to rail franchising after the failure of the West Coast procurement begun in 2010,^[18] and a reset of the £61 billion Network Rail improvement plan from 2012.^[19]

Disability Champion

From 2015 to 2020 he was Disability Champion for the Civil Service.^[20]

Home Office

On 27 February 2017, it was announced that Rutnam would replace Mark Sedwill as Permanent Secretary at the Home Office.^[21] with the Cabinet Secretary, Jeremy Heywood, noting his “strong track record of leadership and achievement”.^[22] Rutnam took up the post in April 2017.^[23] He oversaw the Home Office response to the Grenfell Tower Fire,^[24] the Windrush Scandal,^[25] and series of terrorist attacks between 2017 and 2018,^[24] as well as the rollout of the European Union Settlement Scheme^[25] and preparations for Brexit.^[26]

Following the Windrush Scandal he said he deeply regretted not identifying this as a systemic issue and that the department had not understood enough about the population affected.^[27] On 29 April 2018 Amber Rudd resigned as Home Secretary because she had claimed that there were no targets for removals and then, when it turned out there had been targets, she claimed to have been unaware that they existed.

Rutnam was appointed a Knight Commander of the Order of the Bath in the 2018 New Year Honours for public service.^[28]

Resignation

On 29 February 2020 Rutnam announced his resignation, stating publicly that he would sue the Government for constructive dismissal. In his statement he said: “One of my duties as Permanent Secretary was to protect the health, safety and wellbeing of our 35,000 people. This created tension with the Home Secretary, and I have encouraged her to change her behaviours. This has been a very difficult decision but I hope that my stand may help in maintaining the quality of government in our country, which includes hundreds of thousands of civil servants loyally dedicated to delivering this government’s agenda”.^[29]

Sir Mark Sedwill wrote in his official response that he regretted his decision, saying that he was "grateful for your devoted public service and excellent contribution over the course of your long and distinguished career in the Civil Service...you have ever been mindful of the Civil Service values, demonstrated in the way you have conducted yourself in your roles.”.^[30]

A report by Sir Alex Allan, the Prime Minister's Independent Advisor on Ministerial Standards, later concluded that Priti Patel's approach "amounted to behaviour that can be described as bullying" and that she had "not consistently met the high standards expected of her".^[31]

On 4 March 2021, the Government announced that it had settled Rutnam's legal claims. It later confirmed that the value of the settlement was approximately £376,000,^[32] and that the claims had been for unfair dismissal due to making protected disclosures under whistleblowing laws and/or health and safety law.^[33]