Cabinet secretary Sir Mark Sedwill must ensure that ministers and special advisers are fully aware of the civil service code and staff are clear about how to raise grievances if their political masters ask them to break the law, the Prospect union has said.

In a strongly-worded letter to Sedwill, Prospect deputy general secretary Garry Graham said members of the professionals’ union were “expressing increasing concerns” that prime minister Boris Johnson’s actions and words were jeopardising their ability to do their jobs.

His letter comes after FDA general secretary Dave Penman wrote to prime minister Boris Johnson urging him to "categorically and publicly assure" civil servants that they will not be asked to breach their obligation under the civil service code to 'comply with the law and uphold the administration of justice'."

Graham said the prime minister’s refusal to categorically state that he would abide by the letter of new legislation requiring him to seek an extension to avoid a no-deal Brexit on 31 October if it has not been approved by parliament was placing civil servants in an impossible position.

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Graham’s letter said Wednesday’s decision by the Court of Session in Edinburgh that Johnson’s prorogation of parliament was prompted by improper motives compounded civil servants’ concerns that they would be pressured to support ministers to break the law. The Supreme Court will consider the case in London next week, along with an appeal against a High Court ruling on the prorogation that related to England and Wales.

Graham called on Sedwill to ensure politicians in government and spads understood their obligations under the civil service code and that departmental staff understood their rights – and how to enforce them – as a matter of urgency.

“In these increasingly febrile times it is all the more important that civil servants are supported,” Graham said. “There has not been a government in peace time that has been more reliant on the civil service.

“Over the past number of months, the civil service has been the subject of unwarranted attacks, often fuelled by those seeking to achieve partisan political advantage.

“Against the backdrop of the prime minister repeatedly refusing to confirm that he will abide by the will of parliament and parliamentary legislation, members have raised concerns as to their position as civil servants. These concerns will only be compounded by the judgement from the Court of Session.”

Graham said that while it was “in the DNA” of the civil service to act with integrity, comply with the law, not allow their political impartiality to be brought into question, and to serve the government of the day, it was the job of government to act lawfully.

“The prime minister has not demonstrated or explained how he plans to act in accordance with what is the settled will of parliament,” Graham said.

His letter asked the cabinet secretary to issue guidance to civil servants so they are clear on their rights and responsibilities under the civil service code, and to set out clearly the processes and procedures for staff to follow if they believe they are being to break it.

Graham’s letter said there was an urgent need for Sedwill to “be very clear” that staff should never be asked – or instructed – to act in contravention of the law, and to give a “clear commitment” that staff who raised concerns in good faith would be “supported and not subject to detriment of disciplinary action”.

“Ensuring that civil servants are provided with the appropriate guidance and support has never been more important,” Graham said. “I know that the question of issuing guidance had been a matter of consideration and there was some concern that the issuing of guidance would itself prompt media and political speculation.

“Frankly, we are beyond that point. In order to assure staff and provide clarity, your urgent action is required.”

Graham’s call to Sedwill follows a letter from FDA general secretary Dave Penman to Johnson calling called on the prime minister to “categorically and publicly state” that the government will not ask civil servants to choose between obeying the law and doing their job.

"No civil servant should believe there is a conflict between complying with the law and serving the government of the day – and no prime minister should place the civil service in such an invidious position,” Penman wrote.

At the weekend, foreign secretary Dominic Raab suggested the government would "test" the new no-deal legislation – properly known as the European Union (Withdrawal) (No. 2) Act 2019 – before implementing it.

Penman said: "There should be no grey areas when it comes to the duty to uphold the law and abide by the civil service code. Civil servants should not be placed in a position where they are expected to be, or are seen to be, arbiters of the law.”

Former attorney general Dominic Grieve, one of the authors of the rebel Brexit bill, this week told The Guardian that he understood why civil servants were "getting increasingly worried by the extraordinary words, statements and behaviour coming from No 10 Downing Street".

"Our constitution depends upon people observing rules of honesty and integrity and we seem to be losing them very quickly at present," the ex-Tory MP said.

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