An investigation is under way to determine why problems with coronavirus testing data were not picked up sooner.
Downing Street said there had been a “technical issue” in transferring positive results from labs to central dashboards, leading to nearly 16,000 missing cases.
Public Health England said 15,841 cases between 25 September and 2 October were left out of the UK daily case figures.
Those who tested positive were informed – but their close contacts were not.
The issue has been resolved, PHE said, with outstanding cases passed on to tracers by 01:00 BST on Saturday.
The prime minister’s spokesman said the glitch was “quickly resolved” and NHS Test and Trace and PHE were “urgently contacting” all cases, with extra contact tracers being used.
The technical issue also meant the daily case totals reported on the government’s coronavirus dashboard over the past week have been lower than the true number.
BBC health editor Hugh Pym said daily figures for the end of the week were “actually nearer 11,000”, rather than the roughly 7,000 reported.
Labour described the glitch as “shambolic”.
It was caused by some data files exceeding the maximum size, and issues in transfer of data between NHS Test and Trace and PHE.
Health Secretary Matt Hancock is due to update Parliament on Covid-19 on Monday afternoon.
Prime Minister Boris Johnson said the cases data had been “truncated” and “lost”, but added all people who had tested positive had been contacted, with tracers were “now working through all the contacts”.
The BBC has been told by senior public health officials in the north-west of England that a significant proportion of the unreported cases are from the area.
Cities such as Liverpool and Manchester already have among the highest infection rates in the country, at about 10 times the national average.
BBC analysis found the number of cases reported for the week to 1 October increased by 92.6% in the North West after taking in the missing tests – with similar rises reflected across England.
The increase, of 8,348 cases, is mostly down to the missing tests, but the figures also included some results which came back after 2 October.
At a time when the testing system has come under intense scrutiny after reports of delays and a system struggling to keep up with demand, the latest revelation could not have come at a more awkward moment for the government at Westminster.
Because the nearly 16,000 extra positive test results had been not entered into the test and trace system, their recent contacts were not immediately followed up.
Experts advise that ideally contacts should be tracked down within 48 hours.
Officials say the technical problem has been resolved, with all the new cases added into totals reported over the weekend.
But all this will hardly improve public confidence in the testing system in England.
And it muddies the waters for policy makers and officials trying to track the spread of the virus at what the prime minister has called a “critical moment”.
On Sunday, the government’s coronavirus dashboard said that, as of 09:00 BST, there had been a further 22,961 lab-confirmed cases of coronavirus in the UK, bringing the total number of cases in the UK to 502,978.
Another 33 people were reported to have died within 28 days of testing positive for Covid-19 as of Sunday.
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Public Health England’s interim chief executive Michael Brodie said a “technical issue” was identified overnight on Friday, 2 October in the process that transfers Covid-19 positive lab results into reporting dashboards.
He said the majority of the unreported cases had occurred in the “most recent days”.
“We fully understand the concern this may cause and further robust measures have been put in place as a result,” he said.
PHE said NHS Test and Trace have made sure there are enough contact tracers working, and are working with local teams to ensure they also have sufficient resources to be urgently able to contact all cases.
The number of call attempts is being increased from 10 to 15 over 96 hours.
There have been clear problems with the government’s Test and Trace data, but they do not change our view of the UK’s trajectory.
Cases surged at the beginning of September, they may still be climbing, but not as quickly as anticipated just a few weeks ago.
This perspective comes from three key sets of data – the Office for National Statistics, the React study by Imperial College London and the Covid symptom tracker app.
None are blighted by either the current issues with the Test and Trace data or by people struggling to access a test.
The real fallout of the weekend’s statistical chaos is not the numbers, but the people who should have been contact-traced, told to quarantine and instead may have been unwittingly passing on the virus.
Labour’s shadow health secretary Jonathan Ashworth said: “This is shambolic and people across the country will be understandably alarmed.”
He called for Health Secretary Matt Hancock to explain “what on earth has happened” and what he plans to do to fix test and trace.
Bridget Phillipson, shadow chief secretary to the treasury, told BBC Breakfast she wanted to know whether it had had “any impact on government decision making around local restrictions”.
PHE data shows Manchester now has the highest rate of infection in England, at 495.6 cases per 100,000 people in the week to 1 October, from 223.2 the week before.
Liverpool has the second highest rate, up to 456.4 from 287.1 per 100,000. Knowsley in Merseyside, Newcastle, Nottingham, Leeds and Sheffield have also seen sharp rises.
From 25 Sept to 2 Oct
50,786 Cases initially reported by PHE
15,841 Unreported cases, missed due to IT error
8 days of incomplete data
1,980cases per day, on average, were missed in that time
48 hoursIdeal time limit for tracing contacts after positive test
Source: PHE and gov.uk
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