Almost 600m lateral flow tests given to the public in England may not yet have been used, according to a report that says the hugely expensive test-and-trace system is still bedevilled by problems.

The National Audit Office said NHS Test and Trace (NSHT&T), which Boris Johnson promised would be world-beating and has a budget exceeding that of the Department for Transport, was struggling with some “fundamental parts” of its role.

In a move to help track and suppress the spread of coronavirus, NHST&T distributed 691m quick-result tests to people across England with the aim of helping people to return to workplaces.

The NAO said %results from only 14% of them had been registered, meaning almost 600m had gone unaccounted for.

“NHST&T does not know whether the tests that have not been registered have been used or not,” the report says. “It has started a programme of research to understand why the registration of test results is so low and is working to increase public awareness of the need to register results and improve its ability to track tests.”

The startling finding will increase scrutiny of the test-and-trace system, which was hailed by the prime minister as a vital part of the government’s plan to beat coronavirus, and of its former head Dido Harding, who is seeking to become the next head of the NHS.

The shadow health minister Justin Madders said the report was damning. “If lateral flow tests are going to play their part in helping society reopen, ministers need to make sure results are registered. The British people have sacrificed so much. The government needs to step up,” he said.

The report, which examines NHST&T from November 2020 to April this year, questions the efficiency of the system when it is under strain.

It highlights how the system’s performance in returning the results of tests taken in the community within 24 hours “fell well below its target” during the winter spike in coronavirus cases in December. Only 17% of people received their results within a day in December, compared with 90% by April.

Auditors said the government had advised that it was desirable that no more than 48 hours should elapse between identification of a case and their contacts self-isolating. “In-person PCR tests make up a declining minority of tests, and it is less clear whether the wider system is operating as quickly as it needs to,” the report says.

Meg Hillier, the Labour chair of the public accounts committee, said it was “deeply disappointing” that the test-and-trace system was plagued by many of the same problems that were identified earlier this year.

“NHST&T needs to get to grips with some fundamental parts of the process, such as its timeliness in reaching contacts for all the tests it provides, people coming forward for tests when they have symptoms, and compliance with self-isolation,” she said.

“Meanwhile, budget remains unspent despite the continued use of costly consultants and high levels of unused capacity in the system. As we learn to live with Covid, NHST&T must urgently improve performance to deliver the effective test and trace system we so badly need.”

Test-and-trace programmes for Covid-19 aim to reduce infections by identifying individuals with the virus, tracing their contacts and isolating them to limit further transmission.

Auditors found that NHST&T, allocated a budget of £22.2bn, underspent by more than £8bn following a slump in demand for testing in January and February this year during the national lockdown.

The percentage of paid time that contact centre staff spend speaking to people who should consider self-isolating remains low, the report says. “The utilisation rate for its contact-tracers and other contact centre staff … has generally remained well below the 50% target, peaking at 49% in January 2021 and falling to around 11% in February,” it adds.

Despite previous criticism over the use of expensive management consultancies, NHST&T said it anticipated that the amount recorded as consultancy spend would increase. “NHST&T estimated that it had spent £372m on agency and contractor staff and £195m on consultancy fees, compared with £52m on permanent and seconded staff,” the report says.