Boris Johnson and his closest aide, Dominic Cummings, have been facing a backlash over the dismissal of senior advisers as the union representing high-ranking public servants announced that it was pursuing a case for unfair dismissal and sex discrimination against a female adviser who was sacked and marched out of Downing Street by an armed policeman.

Two days after Sajid Javid resigned as chancellor after refusing a demand from Johnson to sack all his special advisers, the FDA (formerly the First Division Association) told the Observer it expected Johnson and Cummings to give evidence under oath to an employment tribunal in a case involving former Treasury aide Sonia Khan.

The announcement of action by the FDA on behalf of Khan was seen as a warning to Johnson of serious legal consequences and further potential actions if Cummings is not reined in.

Javid resigned after Johnson pushed him to sack advisers Read more

It came as the cull of aides at the top of government increased on Saturday with the sacking of two more special advisers from the No 10 policy unit, Christopher Brannigan and Elliot Roy.

With a culture of fear spreading in Whitehall, the FDA’s general secretary, Dave Penman, said it was up to the prime minister to explain what had happened to Khan, and it was his responsibility that staff were treated decently.

He said: “At the time of Sonia Khan’s dismissal, in the Cabinet Office only the prime minister had the authority to dismiss her. In the employment tribunal we will expect both the prime minister and Dominic Cummings to give evidence under oath as to the reasons for dismissal, the process they applied and the evidence they used to make that decision. They may also be subject to cross-examination on this evidence.

“Special advisers deserve to be treated fairly and with respect. The prime minister is the minister for the civil service and therefore his actions – and the actions of those to whom he delegates – have implications for the entire service.”

Khan, who was Javid’s media adviser at the time she was sacked, was escorted from No 10 by an armed police officer after Cummings accused her of misleading him over her contact with individuals close to the former chancellor Philip Hammond. She denied any inappropriate contact. Javid was furious to learn about her dismissal after the event.

It is understood that Cummings faced criticism at a weekly meeting of advisers on Friday night, the day after the reshuffle. Lynn Davidson, a former Sun journalist, who advises the defence secretary, Ben Wallace, reportedly told him he had been out of order and had to show more respect to people who were “doing their best in incredibly difficult circumstances”.

At the advisers’ weekly meeting the previous Friday, it is claimed that Cummings humiliated young aides to Theresa Villiers and Andrea Leadsom, asking them deliberately detailed and difficult questions he knew they would struggle to answer. Six days later, Villiers and Leadsom, and with them their two advisers, were sacked in the reshuffle.

Sources said Cummings had yet to file a response to the claims about Khan by the FDA and its lawyers. While the union said it expected Johnson and Cummings to give evidence under oath, it is thought likely that the case will be settled before a hearing, by means of a financial or other settlement. In 2012 a senior civil servant received a payout of £25,000 in a bullying case she took against Cummings and a senior member of Michael Gove’s team when Cummings was a special adviser at the Department for Education. An internal investigation found no grounds for disciplinary action.

At the time of Khan’s dismissal last September, the terms of employment for special advisers made it clear that it was only the prime minister who had the power to sack them. This was then changed after Khan left, giving Cummings ultimate “responsibility for disciplinary matters”.