Care home inspectors only started asking if residents were dying from Covid-19 last Thursday, two and half weeks after the UK went into lockdown and a month after the World Health Organization declared a global pandemic, the Guardian can reveal.

Until 6 April, the Care Quality Commission did not ask for information on coronavirus deaths and only started doing so when it realised the information coming back was out of line with reports of a rising death toll.

Labour said the revelation was “extraordinarily worrying” as it emerged the CQC had previously admitted to shortcomings in how it gathers data about deaths in care.

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The delay in asking for specific information about Covid-19 deaths may explain why official figures for deaths in care have so significantly understated reality. On Wednesday, Prof Martin Green, the chief executive of industry group Care England, said the virus has claimed at least 1,400 lives in care settings. Fifteen deaths were reported at a single care home in Wavertree, Merseyside, and eight at a home in Stowmarket in Suffolk.

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Twenty-four hours earlier, the Office for National Statistics (ONS) said there were 217 deaths in all care homes in England and Wales up to 3 April, based on death certificates. CQC data, which should be delivered more promptly but is so far considered incomplete, has not yet been published.

By law, care homes must promptly report deaths to the CQC but until last week were not asked whether it was Covid-19 related. A tick box for confirmed or suspected coronavirus was only added the day before the Easter break, by which time more than 6,000 people had died from the virus in NHS hospitals and hundreds more in care homes.

The shadow minister for social care, Liz Kendall, said it was “extraordinarily worrying” that the CQC did not ask about Covid-19 until Easter “when we knew care homes in other countries have experienced very high levels of deaths”.

“The whole system should have moved much more quickly to find out what was happening to the most vulnerable people in society,” she said.

The CQC denied that it was a failure not to start asking for information about Covid-19 deaths earlier in the crisis.

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“Across the world people have had to reset their data to include care homes,” a spokeswoman said. “It was clear that what we were seeing [in the data] didn’t reflect what we were hearing from providers and we wanted to make it clearer.”

The regulator said homes could have written “Covid-19” or “suspected Covid-19” in the free text box but many did not and some left it blank.

Helen Whateley, the care minister, said on Wednesday the government accepted that official figures have understated the scale of the problem.

“We are working really hard to make sure we do have the full picture and we do have updated data of lives lost,” she said. “I don’t want to speculate about what numbers might be. Having robust and accurate data is really important for decision-making. ONS and the Care Quality Commission are working to get up-to-date figures.”

The CQC and ministers were warned in 2018 about weaknesses in the way the regulator gathers data on care home deaths and it admitted there were problems, the Guardian has learned.

Matt Oakley, who runs a firm making a medical anti-choking device, raised the alarm after struggling to find out about deaths in homes from choking. He told the CQC in Feb 2018 “that due to the way data is stored the CQC are unable to establish wider trends, issues or patterns”.

Andrea Sutcliffe, the then chief inspector of adult social care, replied admitting: “We have a gap in our ability to use the information on the specific cause of death … more widely which could help us in our purpose of encouraging services to improve.”

She said “whilst we are able to examine trends on the number of deaths … we cannot currently perform this level of analysis by cause of death … to establish more detailed trends”.

Oakley raised the issue with Caroline Dinenage, then health and social care minister, but her ministry referred him back to the CQC.