Members of the public have been urged to book for further testing after 43,000 PCR tests at government-run sites resulted in false negatives.
NHS Test and Trace have suspended testing operations provided by Immensa Health Clinic Ltd at its laboratory in Wolverhampton, following an investigation into reports of people receiving negative PCR test results after they have previously tested positive using lateral flow tests.
The majority of those affected appear to be from the south west of England, but people in Wales and the south east are also understood to be impacted.
An investigation led by the UK Health Security Agency (UKHSA) is underway attempting to confirm the cause of the problem, but early indications predict that more than 10 per cent of the 400,000 samples processed by the lab could be wrong.
The agency estimated 43,000 people may have been given incorrect negative PCR test results between Sep 8 and Oct 12.
A spokesman said: "This is an isolated incident attributed to one laboratory but all samples are now being redirected to other laboratories."
NHS Test and Trace is now contacting the people that could still be infectious to advise them to take another test.
Close contacts who are symptomatic will also be advised to take a test in line with normal practice.
It comes as West Berkshire Council said in a statement some of the tests at the Newbury Showground testing site, operated by the Department for Health and Social Care (DHSC), "have had results sent out that may have incorrectly shown as negative for Covid-19".
"After receiving reports from local residents in recent weeks that there were concerns about the accuracy of test results from the site, we passed these concerns onto the DHSC for further investigation," the statement added.
"The DHSC has now confirmed that a number of sites nationally may have been affected by this issue, including the one at Newbury Showground."
Those who received a negative result for a PCR test between Oct 3 and 12, as well as their close contacts, were "strongly" encouraged by the local authority to take another test.
Councillor Graham Bridgman said: "Testing continues to remain important as we learn to live with Covid and anyone who has symptoms, or who has been in contact with someone who tests positive, should book a PCR test straightaway. We also strongly encourage the public to do twice weekly lateral flow testing.
Dr Will Welfare, Public Health Incident Director, UKHSA: "We have recently seen a rising number of positive LFD results subsequently testing negative on PCR.
"As a result of our investigation, we are working with NHS Test and Trace and the company to determine the laboratory technical issues which have led to inaccurate PCR results being issued to people.
"We have immediately suspended testing at this laboratory while we continue the investigation.
Andrea Riposati, CEO of Immensa Health Clinic Ltd, said: "We are fully collaborating with UKHSA on this matter. Quality is paramount for us.
"We have proudly analyzed more than 2.5million samples for NHS Test and Trace, working closely with the great teams at DHSC and UKHSA.
"We do not wish this matter or anything else to tarnish the amazing work done by the UK in this pandemic."