Bullying allegations engulfing the home secretary, Priti Patel, have intensified as it emerged that “major run-ins” had forced the resignation of one of her department’s most senior civil servants on immigration.

Union sources have revealed that “uncomfortable” demands by Patel had prompted Mark Thomson, the director general of UK Visas and Immigration and HM Passport Office, to announce his departure just weeks after her appointment.

Mick Jones of the Public and Commercial Services Union (PCS), the largest trade union for Home Office staff, said that Patel’s approach to various immigration issues had led to Thomson’s resignation.

“He’s indicated to our reps that it was mainly because they had had major run-ins. It was clear that [Patel] had come in and was trying to do things that they [Home Office officials] just weren’t comfortable with and [Thomson] sort of said ‘I’m off then’.”

Last week it was reported that Patel allegedly questioned why police could not use force against Extinction Rebellion protesters.

Patel became home secretary in July last year. Thomson told colleagues he was leaving the following month after five years at the department. However Home Office sources last night said Thomson had decided to leave before Patel was appointed in order to “pursue other career opportunities”.

In another development that will increase pressure on Patel, the Observer understands that a Home Office employee who collapsed recently following a testy meeting with Patel was another of the department’s most senior civil servants.

The top-level immigration enforcement official is believed to have fallen ill after working through the night attempting to reverse a high court ruling barring the deportation of foreign criminals to Jamaica. He was taken to hospital and found to have a sodium deficiency.

The man, whose career has been based entirely within the Home Office and where he has been private secretary to six ministers, is, like Thomson, widely respected within the department. He leads more than 5,000 staff responsible for ensuring immigration law is adhered to.

Last week Patel unveiled the government’s new immigration policy which drew fierce criticism from UK businesses. Patel claimed that eight million “economically inactive” British adults could be given the skills to do jobs in sectors where there were shortages as a result of the new points-based system. But analysts said that most of these were students, sick, looking after relatives or retired.

Last week the Times reported multiple Home Office sources accusing Patel of bullying, belittling officials and presiding over an “atmosphere of fear”. Among the allegations into a “pattern” of bullying behaviour were claims of attempts by Patel to oust her permanent secretary, Sir Philip Rutnam. Jones confirmed that the PCS was in regular contact with Rutnam, whom he described as receiving “harsh treatment”. The home secretary, however, had “not shown much appetite” for working with the union, according to Jones.

Information on the government’s website about Thomson’s position underlines its importance, stating: “Mark has responsibility for making millions of decisions every year about who has the right to visit or stay in the country.”

On Friday, the Times reported that concerns over Patel’s behaviour had been aired as far back as 2017 when she drew complaints from officials when she was a minister in the Department for Work and Pensions.

When Thomson first announced last August that he would be leaving the Home Office, he sent staff an email that read: “The sharp-eyed amongst you may notice that my job has been advertised today. I wanted to let you all know that after five years in the Home Office I have decided the time has come for me to move on.” At the time, the Home Office issued a statement saying he was to “leave his post in March 2020 for personal reasons”. When the bullying allegations emerged, it said that there had been no “formal” complaints against Patel.

Some have leapt to her defence. Business minister Nadhim Zahawi said she was a “brilliant, collegiate team player”.