Unions have condemned a planned change to Whitehall rules meaning civil servants must ignore Strasbourg judgments halting Rwanda deportation flights. Home Office staff removing asylum seekers will be told to implement last-minute injunctions from the European court of human rights (ECHR) only if ordered to do so by a minister, according to official guidance. Three civil service unions say this will mean that senior civil servants and Border Force staff will have to choose between breaking international law, disobeying the instructions of a minister or resigning. In a further development, the Guardian has learned that the first civil service commissioner, Gisela Stuart, was not consulted about the plans. It would be considered “best practice” for the head of the independent statutory body to be consulted before significant changes to Whitehall rules. Sir Matthew Rycroft, the permanent secretary in the Home Office, confirmed the change in a published exchange of letters with a senior Cabinet Office mandarin. In the document, he wrote that staff should in future seek approval from ministers if they receive rule 39 indications – so-called “pyjama injunctions” – from Strasbourg. “I can confirm that we shall issue guidance to those involved in removals to Rwanda, and revised guidance to caseworkers,” Rycroft wrote. “This will amend the existing Home Office guidance in relation to removals under the Illegal Migration Act and safety of Rwanda bill that says: ‘Where you have been notified that a R39 indication has been made, you must defer removal immediately.’ “Home Office officials shall proceed with removal if the relevant minister approves that course of action.” The guidance came hours after the minister for countering illegal migration, Michael Tomlinson, said ministers were planning to tweak the civil service code to order officials to follow ministerial decisions. Downing Street sources later downplayed the move as a change to the civil service code, instead saying the government would change guidance. Dave Penman, the head of the FDA union, said that changing either the code or guidance would not alter the obligations of senior civil servants to work within the law. “Changing guidance or changing the civil service code does not change the facts,” he said. “If the ECHR rules a deportation unlawful, those are the facts of the case. “Ministers are trying to put civil servants in an invidious position by placing them between serving ministers and their professional obligations. It looks as if ministers are trying to avoid leaving the ECHR and are asking civil servants to break the law instead. “What must be remembered, however, is that ministers under their own code have the obligation not to put civil servants in a position where they are in breach of the civil service code.” Mark Serwotka, the general secretary of the PCS union, said: “This latest ruse by ministers is symptomatic of their desperation to keep their unlawful, unworkable and inhumane Rwanda scheme on life support. “In continuing to push the scheme, ministers are acting unlawfully. Now they appear to be trying to force civil servants to do the same. “PCS will not allow it to stand. Our legal challenge to the Rwanda scheme led to the supreme court declaring the scheme unlawful. We will not hesitate to take further action through the courts to defend our members from this latest attack.” Garry Graham, the deputy general secretary of Prospect, said: “This in effect could put civil servants in an impossible position where the choice is potentially between breaking international law, disobeying the instructions of a minister and facing potential disciplinary action or resigning. “This is a problem of the governments own making and they should not be putting civil servants in this invidious position.” Adam Wagner, a human rights lawyer, said plans to amend the civil service code were “obviously a non-starter”. “Civil servants can only advise on the basis of the law, and the government’s advice from the attorney general and [barrister] Sir James Eadie apparently is, rightly, that rule 39 measures must be complied with in order not to breach the UK’s duties under the European court of human rights,” he said. “So it’s not civil servants who make these decisions, and amending the civil service code won’t make any difference.” Rishi Sunak is seeking to win over Tory rebels before Wednesday night’s vote on his Rwanda plan after facing the biggest Conservative revolt of his leadership. Two deputy party chairs and a ministerial aide quit to join the ranks of the Tory rebels in the Commons on Tuesday night. Sixty Conservatives supported changes to the safety of Rwanda bill put forward by the Tory veteran Sir Bill Cash, as rightwingers pushed to ensure UK and international law cannot be used to prevent or delay a person being removed to Rwanda.