Several councils did not have access to all the latest data for almost three weeks, the BBC learns.
Failures in England’s Test and Trace system are partly responsible for a surge in the Indian variant in one of the worst affected parts of the country, a report seen by the BBC says.
For three weeks in April and May, eight local authorities in England did not have access to the full data on positive tests in their area.
The number of missing cases was highest in Blackburn with Darwen, Lancashire.
A recent surge in infections there has been linked to the Indian variant.
The government said a “small number” of people in contact with those who tested positive for coronavirus had “experienced a temporary delay in getting a message from NHS Test and Trace”.
The other areas affected by what is thought to have been a technical glitch were Blackpool, York, Bath and North East Somerset, Bristol, North Somerset, Southend-on-Sea and Thurrock.
Labour called on ministers to “explain what’s gone wrong”.
NHS Test and Trace – for which £37bn has been set aside – identifies people who have been in close contact with someone who has caught Covid.
Between 21 April and 11 May, the system only provided details of a limited number of positive cases of coronavirus to the eight local authorities.
On 11 May, they were told by the Department of Health and Social Care that, over that period, 734 positive tests had not been reported.
According to a report by officials at one of the councils affected, the central Test and Trace system failed to notify its staff of cases, meaning their contacts could not be traced locally.
It says that “the rapid spread of Indian variant cases… may be partially or largely attributable to risks in the international travel control system”, adding: “These were exacerbated by the sporadic failure of the national Test and Trace system.”
Six of the local authorities affected have confirmed to the BBC that they experienced problems.
Although it is thought that the people tested were given their results, local authority staff were not provided with contact-tracing information through the central system.
Some 2,967 cases of the Indian variant – which is believed to spread more quickly than the Kent variant that caused the winter spike in infections – have now been identified in the UK.
In the latest government figures – which cover all forms of Covid – a further 2,874 people have tested positive, and seven new deaths were reported.
The government added India to the “red list” of countries, from which travellers must quarantine in a hotel on return, on 23 April – two days after the problems with Test and Trace started.
While national contact-tracing teams should take on variant cases, identifying the particular variant can take up to two weeks.
In the meantime, local authority staff are often the first to make contacts with positive cases.
Where cases went unreported, they were also in many cases unable to offer support to isolating individuals.
image copyrightJohn Fairhall/BBC
The Department of Health told Blackburn with Darwen Council that there were 164 cases it had been unaware of. The people affected were subsequently traced.
Another 130 cases were not reported, but, because they had passed the 10-day isolation period, could not be followed up.
Even when cases were uploaded to the system on 12 May, some key information, such as phone numbers or addresses, was incomplete.
For Labour, shadow health secretary Jonathan Ashworth said it “beggars belief” that councils had been “left in the dark for two weeks when we know acting with speed is vital to containing an outbreak”.
He added: “Ministers need to explain what’s gone wrong and provide local health directors with all the resources they need to push infections down.”
Liberal Democrat MP Layla Moran, chair of the All-Party Parliamentary Group on coronavirus, said “grave errors” over Test and Trace failures had “contributed to the surge in cases of the Indian variant”.
A Department of Health and Social Care spokesman said: “A small number of contacts of positive cases experienced a temporary delay in getting a message from NHS Test and Trace.”
They added: “NHS Test and Trace has contacted over 10 million people since the start of the pandemic, dramatically reducing the potential spread of the virus.
“A small number of contacts of positive cases experienced a temporary delay in getting a message from us recently but it was resolved quickly. All individuals were contacted and instructed to self-isolate for 10 days.”