The UK will “imminently” ask the European Court of Human Rights to reconsider a measure that blocked some asylum seekers from being removed on the first planned Rwanda deportation flight, the High Court has been told.

The expected first flight in the controversial policy was grounded on June 14 after 11th-hour legal rulings, including from the Strasbourg-based court.

In the days leading up to the flight, several asylum seekers had asked for interim relief at the High Court in London and were denied, before some were also denied at the Court of Appeal and the UK Supreme Court refused to intervene.

However, on the night of the flight, judges at the European Court of Human Rights granted interim measures which blocked the removal of three asylum seekers set to be on the plane to Kigali.

In the first interim measure from the European Court of Human Rights, judges said an Iraqi man should not be removed “until the expiry of a period of three weeks following the delivery of the final domestic decision in the ongoing judicial review proceedings”.

Court of Appeal judges also granted injunctions to three asylum seekers, with the court confirming that three judges held an urgent hearing at 9.50pm on June 14 – just 40 minutes before the flight was due to take off.

These injunctions prevented the removal of the men until after a challenge against the decision of Mr Justice Swift to reject their bids to remain in the UK pending the full judicial review of the Rwanda relocation policy – due to be heard in July.

At a High Court hearing on Monday, the court heard that the Home Office would be challenging the European court’s interim measure – known as a rule 39 indication.

In written submissions, Jack Anderson, for the department, said: “The defendant will resist any further application for a rule 39 indication and, further, the UK will be applying to the European Court of Human Rights to reconsider the rule 39 indication on an urgent basis.

“The UK has informed the European Court of Human Rights that it intends to submit representations imminently, and the European Court of Human Rights has informed the UK that such representations will be considered as a matter of urgency and a response will be received within a few days of receipt.”

Mr Anderson also said the Home Office will argue that Court of Appeal judges wrongly granted interim relief “on the basis” of the European court’s intervention.

The news of the challenges came in written submissions made by the Home Office as part of claims brought by other asylum seekers at risk of being removed to Rwanda.

During Monday’s hearing, Mr Justice Swift denied bail to three asylum seekers bringing legal challenges against the deportation policy, pausing other aspects of the claims until after the judicial review.

A Court of Appeal hearing is now expected on June 28, with a case management hearing for the judicial review of the policy due on Wednesday.