The app, which has been available for download across England and Wales since Thursday, has been hailed by Health Secretary Matt Hancock as an “important step forward” in the fight against the virus.
But only tests carried out by private outsourcing companies like Serco and Deloitte are currently giving people the code that lets them input results into the app.
This means that potentially tens of thousands of negative and positive results delivered by NHS hospitals, Public Health England laboratories or as part of the Office for National Statistics survey are not being registered on the app.
Tests at these public facilities are reserved for people in clinical need and health and care workers, according to the Government. Tens of thousands of these “Pillar One” tests are carried out each day, official data shows.
The Department of Health and Social Care (DHSC) said it is aware of the issue and “urgently working” to resolve it.
The app is supposed to help people manage the risk of being infected by telling them if they have been close to anyone who has tested positive for the virus.
The issue was raised when someone who said he had been tested for the virus wrote on Twitter that he had not been able to register his result.
The app’s support team Twitter account replied to him and said: “If your test took place in a Public Health England lab or NHS hospital, or as part of national surveillance testing conducted by the Office for National Statistics, test results cannot currently be linked with the app whether they’re positive or negative.”
A DHSC spokesman said: “We are urgently working to enable positive tests for people who aren’t already given a code to be added to the Covid-19 App.
“NHS Test and Trace will continue to contact people by text, email or phone if your test is positive, advising you to self-isolate and for those who don’t have a code the contact tracers will shortly be able to provide codes to insert in the app.
“If you book your test via the app the results will be automatically recorded in the app and the isolation countdown will be updated.”
Shadow Health Minister Jonathan Ashworth replied to the original tweet, asking: “Have they really launched an app that doesn’t actually link to tests carried out by NHS hospital labs & PHE labs instead only including tests carried out via the outsourced lighthouse lab network??”
The app has also come under fire for a function that only enables people to input positive results.
The DHSC told the BBC that the app would be updated.
Officials have said people who are unable to use the app should continue to use the other contact tracing services provided by NHS Test and Trace.