Imagine the archetypal career civil-servant, and Philip Rutnam is it. Privately schooled and educated at Trinity College, Cambridge, and Harvard University, the 54-year-old has always been considered unflappable and discreet. And when he was named in 2018’s new year honours list for his “public service”, Rutnam was on a roll. The previous year, he had been rewarded for three decades in the civil service with a move to the post of permanent secretary in the heavyweight Home Office, managing 35,000 staff as well as immigration and security at a time of Brexit and a heightened terror threat.

Lord Kerslake, the former head of the civil service who appointed Rutnam to the post of permanent secretary at the Department of Transport in 2012, described him as “just the kind of person a minister needs in a department like the Home Office”.

But in July 2019, the Home Office was to undergo a change of leadership. Out went Sajid Javid; in came Priti Patel, after 18 months on the backbenches following her acrimonious ousting by Theresa May as international development secretary.

There was a brief period of calm. It didn’t last long. Tensions steadily escalated and led, eventually, to Saturday’s explosive announcement by Rutnam. Not only was he resigning, he was suing the government for constructive dismissal. He had received allegations that Patel had sworn at, belittled and acted unreasonably to staff. It was behaviour, he said, “that created fear and that needed some bravery to call out”. He added: “My experience has been extreme, but I consider there is evidence it was part of a wider pattern of behaviour.” These claims have been denied.

Sources yesterday confirmed that Rutnam was far from the only person to have clashed with Patel, with many senior Home Office officials having had “run-ins” with her. A source close to the home secretary, however, argued that these officials had simply wanted to introduce a new work ethic and found that not everyone felt the same. The source, asking not to be named, admitted that their approach may have “pissed people off”.

Home Secretary Priti Patel. Philip Rutnam says he will sue for constructive dismissal. Photograph: Dominic Lipinski/PA

The first signs of trouble appeared within weeks of Patel’s arrival. Last August, one of Rutnam’s most senior colleagues, Mark Thomson, the director general of UK Visas and Immigration, announced that he was leaving. He told the Public and Commercial Services union (PCS) that Patel was “coming in and doing things we weren’t comfortable with”. The Home Office claims that Thomson had decided to resign before Patel arrived, but has not provided evidence for this.

By late October, Thomson had met with union officials and discussed a “breakdown” in relationships between Patel and senior civil servants. Tensions continued to rise. As the general election was announced, Patel wanted to appoint a new Home Office team, one that appreciated her hardline outlook on issues such as immigration. Members of her team now admit, with hindsight, that “perhaps we could have gone a bit slower”.

As it was, Andy Tighe, who had been at the Home Office since 2011, and was communications director from 2017, felt he had become a target. The former BBC journalist, who was highly regarded by journalists in the parliamentary lobby, was considered by Patel’s team to have become “too hands-off”. Patel reportedly tried to sack Tighe on Christmas Eve. Rutnam was aghast, and though Tighe tried to hold on, he left in February.

“There was nothing personal against Andy, though I think it was taken like that, which I understand,” said a Whitehall source.

Just the kind of person a minister needs in a department like the Home Office Lord Kerslake on Rutnam

Others have said that Dominic Cummings, the prime minister’s closest aide, who has promised to reform the entire Whitehall machine – which he says acts as a break on radicalism – further emboldened Patel to take on Rutnam following the election.

“In focus groups, they say it’s good that the civil service is working hard, and that is what Dom Cummings basically says,” said an advocate of Patel. Cummings is currently under pressure to give evidence under oath to an unfair dismissal employment tribunal involving the former Treasury aide Sonia Khan, who was sacked and marched out of Downing Street by an armed policeman.

The new year brought little respite for Rutnam and his colleagues. In early February, another “heated” meeting with Patel and senior immigration officials over a deportation court case to Jamaica saw a high-ranking civil servant collapse after working overnight. The incident is said to have left officials in despair.

Briefings against Patel became more pointed. One report suggested that MI5 did not trust the home secretary, though MI5 has disputed this. Patel’s supporters fought back, launching what Rutnam dubbed a “vicious and orchestrated” campaign against him.

Any semblance of protocol has been abandoned. Usually such clashes are managed quietly behind the scenes until the civil servant is discreetly ushered into a new role. Sources pointed to the case of Helen Ghosh, who, as permanent secretary at the Home Office, reportedly clashed with May, the then home secretary. The situation was neatly resolved when Ghosh stepped down in November 2012 to become director general of the National Trust.

The former cabinet secretary Lord Turnbull, who was head of the civil service and cabinet secretary between 2002 and 2005, said he had never heard of a dispute involving a secretary of state and permanent secretary being allowed to intensify in a way that held such potentially serious consequences for the civil service.

“Normally when there is an issue, a way would be found to secure a judicious job swap or some other route to resolve the difficulty. For this to have got to this stage is extraordinary and potentially extremely damaging,” said Turnbull.

Rutnam, too, could have bided his time and held on for a new position. Or he could have resigned and gone quietly with financial compensation. It appears he had seen too much. His unprecedented salvo yesterday was clearly designed to topple Patel. For those Home Office civil servants left behind, some of whom yesterday praised Rutnam’s “courage and integrity”, the issue is not if a successor to Patel is announced – but when.