Rishi Sunak’s flagship plan to send asylum seekers to Rwanda will cost taxpayers £1.8m for each of the first 300 people the government deports to Kigali, Whitehall’s official spending watchdog has disclosed.

The overall cost of the scheme stands at more than half a billion pounds, according to the figures released to the National Audit Office. Even if the UK sends nobody to the central African state, Sunak has signed up to pay £370m from the public purse over the five-year deal.

The disclosures follow nearly three years of refusals by prime ministers, home secretaries and senior Home Office staff to explain the full costs of the deal, citing “commercial confidentiality”.

So far, no asylum seeker has been sent to Rwanda, because of repeated challenges to the scheme under European and UK laws.

Diana Johnson, the chair of the home affairs select committee, expressed her shock at the final figures and expressed serious concerns at the lack of transparency.

Johnson, a Labour MP, said: “These are staggering figures. Huge initial outlay and ongoing costs raise serious questions about how this can be cost-effective, even compared to high hotel accommodation costs.

“What we are left with is a very expensive programme the government hopes may offer a deterrent to those seeking to cross the Channel in small boats. Yet, there is little evidence for this either.

“Unless the government deals with the realities of the situation and focuses its energy and the public’s money on fixing the real issues in the asylum and immigration system, it will achieve nothing.”

The Home Office has agreed to make two types of direct payments to the government of Rwanda, auditors said. The UK will pay to the economic transformation and integration fund (ETIF), which is designed to support economic growth in Rwanda; and make payments to cover asylum processing and operational costs for individuals relocated to Rwanda.

The Home Office has paid £220m into the ETIF since April 2022, and it will pay further amounts of £50m in 2024-25, £50m in 2025-26 and £50m in 2026-27.

A “five-year processing and integration package” for each relocated person, which covers accommodation, essential items such as food, medical services, educationand other integration programmes has also been agreed, the report said. This will cost up to £150,874 for each deported person.

The figures mean that if the UK sends 300 people to Rwanda, it will cost the taxpayer £490m under the partnership; an extra £6m in individual payments; plus £45m for processing and operational costs over five years. The total costs would be £541m, which works out as £1.8m per asylum seeker.

The Home Office has spent £20m setting up the Rwanda scheme, which has survived the tenure of three prime ministers – Boris Johnson, Liz Truss and Rishi Sunak. Four home secretaries – Priti Patel, Suella Braverman in two separate terms, Grant Shapps and James Cleverly – have overseen the scheme.

Officials expect that £20m to rise to £28m by the end of 2023-24, the report said. The Home Office estimates that it will incur further costs between now and the end of the scheme.

If the UK activates a break clause in the deal, it would stop further payments under the ETIF, but would still have to pay for any deported people’s living costs and no past payments would be recoverable, the report said.

If the Rwandan government breaks the deal, the UK can ask for a reimbursement of payments from that year, but not previous years.

The costs set out in the report are the direct costs associated with the partnership. There are wider costs of implementing the Illegal Migration Act that have not been considered, the report said.

The Home Office claims that the average cost per night of providing hotel accommodation to asylum seekers is £140, which does not include the costs to local services. It says that the estimated total cost to the taxpayer over five years would far exceed £150,000 per asylum seeker.

The impact assessment for the Illegal Migration Act 2023 projects that if nothing is done, the cost of housing asylum seekers will reach £11bn a year by 2026.

A Home Office spokesperson said the scheme was a “bold, long-term solution” and insisted that it would send people to Rwanda and be value for money.

“Doing nothing is not without significant costs – unless we act, the cost of housing asylum seekers is set to reach £11bn a year by 2026. Illegal migration costs lives and perpetuates human trafficking, and it is therefore right that we fund solutions to break this unsustainable cycle,” she said.

“We have a strong relationship with Rwanda and both sides remain absolutely determined to deliver on this partnership. Once the safety of Rwanda bill and treaty are in place, we will focus on getting flights off the ground.”

Yvette Cooper, the shadow home secretary, said: “This report reveals the national scandal the Tories have been trying to hide. Its shocking analysis shows the costs of the failed Rwanda farce are even higher than previously thought.

“In order to send less than 1% of UK asylum seekers to Rwanda on a few symbolic flights, the taxpayer will be forced fork out over half a billion pounds – with no ability to recover any of the money already sent.

“Rishi Sunak has staked his position on this scheme. He must account for this fiasco.”