Dominic Cummings has been handed a new formal power to sack cabinet ministers' advisers, triggering a protest from the head of the civil service union.
New contracts of employment make clear that Boris Johnson’s controversial chief aide now has ultimate “responsibility for disciplinary matters”, rather than individual ministers.
The move follows the furore over the dismissal of Sonia Khan, an aide to the chancellor Sajid Javid, who was frogmarched out of Downing Street by an armed police officer last month.
Mr Cummings claimed said she had misled him over her contact with Philip Hammond, her former boss, but Ms Khan denied any wrongdoing – while Mr Javid was not even consulted.
Dave Penman, the general secretary of the FDA trade union for senior civil servants, said ministers were “allowing their authority to be undermined and publicly”.
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“This is such a critical element of their support network and such a clear message from No 10,” Mr Penman told The Times.
“Disciplinary matters lying with the prime minister and chief of staff is a significant change.
“It cuts across the ministerial code, which says that responsibility for special advisers lies with ministers and ministers are accountable to the government, parliament and the public for their advisers' behaviour.”
The existing “model contract” from December 2016 said that “the responsibility for disciplinary matters rests with your appointing minister”.
Now the special advisers must agree that “the responsibility for disciplinary matters rests with your appointing minister and the prime minister's chief of staff”.
A clause relating to advisers' grievances and appeals against actions has also been updated to give the chief of staff a role, The Times reported.
Mr Johnson has not formally given any adviser the title “chief of staff”, but Mr Cummings is widely seen as performing the role in all but name.
Sir Eddie Lister, who was Mr Johnson's chief of staff as mayor of London, is his chief strategic adviser.
The government is arguing that the changes to the contract simply formalise the longstanding arrangement for special advisers under successive prime ministers.
A spokeswoman said: “As has been the case under successive administrations of all political colours, all special advisers' appointments are approved by the prime minister and they can be dismissed without notice if the prime minister withdraws his consent. The legislation is clear on this point.”
The row comes amid anger that Mr Cummings has been granted a security pass for the Palace of Westminster despite having been found in contempt of parliament.
He was seen in parliament several times earlier this month, at one point reportedly bellowing a challenge at Jeremy Corbyn, the Labour leader, to accept a general election.