UK Taxpayers will continue to pay money to Rwanda as part of the Government’s controversial migrant deportation scheme despite the policy being ruled unlawful, the Home Office’s top civil servant admitted on Wednesday.

Sir Matthew Rycroft, the Home Office’s permanent secretary, said that there were continuing “fixed costs” associated with the deal struck by ministers with the Rwandans to take migrants arriving in Britain in small boats to process their asylum applications.

The policy was ruled unlawful earlier this month by the Supreme Court on the grounds that Rwanda was not a safe country.

But Sir Matthew told the Commons Home Affairs Select Committee that payments would continue under the terms of an Economic and Development Partnership struck between Britain and Rwanda even though no migrants would be going there.

He said the potential bill included money to pay for accommodation in Rwanda for the migrants who are no longer going to be deported, as well as other funds to assist the authorities in Kigali to develop their “capabilities and capacity”.

Sir Matthew refused to say how much extra money will be paid to Rwanda, which has already received £140 million of taxpayers’ money, claiming that the figure was “commercially sensitive” and would only be revealed next summer after his department’s annual accounts are published.

His confirmation that extra payments will be made to Rwanda came as Sir Matthew told MPs that other countries, including Germany which he visited last week for discussions, are interested in Britain’s Rwanda scheme.

He also suggested that the Rwanda scheme, which ministers have argued is key to stopping migrants from crossing the Channel in small boats  – could be playing a part in reducing the flows, saying that the numbers this year were down by a third and that “something is deterring” them.