The United Nations refugee agency has made a dramatic intervention to try to halt Priti Patel’s plan to deport asylum seekers to Rwanda. In a late submission of evidence, the UNHCR claimed the home secretary misled refugees over the organisation’s support for the plan. The agency has also said the scheme failed to meet the required standards of “legality and appropriateness” for transferring asylum seekers from one country to another. It emerged on Friday that the government has cancelled the removal directions for three people who had asked the high court to prevent their deportation. In the hearing, it emerged two more people will also have them cancelled. Letters sent by the Home Office to those seeking asylum assured them the UNHCR was “closely involved” in the scheme to send people to the east African country, the high court was told. But a letter from the UNHCR to the Home Office minister Tom Pursglove questioned this claim. “We are also concerned by statements made in the letters indicating that UNHCR has not expressed substantial concerns with regard to the shortcomings in the capacity of the Rwandan asylum system,” the agency wrote. The letter emerged at the first legal challenge of the policy, which was heard on Friday at the Royal Courts of Justice. The refugee charities Detention Action and Care4Calais and the Public and Commercial Services union have applied for an urgent interim injunction preventing any flights from leaving, including the first, until after its application for a judicial review can be heard. The high court was told the UNHCR had a number of concerns about the asylum process in Rwanda, including discriminatory access to asylum – including for LGBT people – a lack of legal representation and interpreters, and difficulties in launching an appeal. Laura Dubinsky QC, the barrister for the UNHCR, said the refugee agency was concerned about “inaccuracies” in Home Office claims about its involvement in the scheme, saying it “in no way endorses” it and had told the government it believed it to be “unlawful”. Raza Husain QC, for the claimants, said Patel had misrepresented the UNHCR’s position. “These are concerns that have been communicated to the UK authorities and yet the secretary of state’s position … is that the UNHCR has given this plan a green light. That is a false claim,” he said. In court documents, Home Office lawyers urged the court to reject the application, arguing it “fails at the first stage”, adding: “The claimants have not identified a serious issue to be tried, still less the strong case they allege for the grant of relief at trial.” In the papers, Rory Dunlop QC and Mathew Gullick QC for the department said: “The application for interim relief should be dismissed. In the alternative, any order for interim relief should be limited.” The claim and application ran to “many hundreds of pages”, the lawyers said, as they suggested there had been delays in serving the papers, arguing: “Given the volume of material that has now been served, this delay has prejudiced the defendant’s ability to respond to the interim relief application.” The high court is due to hear a further challenge to the policy on Monday, brought by the refugee charity Asylum Aid and supported by the campaign group Freedom from Torture. Downing Street said Boris Johnson was still hopeful the first flight would go ahead on Tuesday. A No 10 spokesperson said: “Yes. You’re aware of the ongoing court case today but we have set out our position on why we think this is the right approach.”