It came as Matt Hancock, the Health Secretary, said it was "terrific" that the health service now has capacity to carry out 39,000 tests a day, even though less than half of those tests were used on Tuesday.

All PHE's 12 centres have been told to stop using the existing tests by Thursday, instead using checks supplied by commercial firms. NHS laboratories still using the method have been told any uncertain results must be double-checked until all have switched to only using such kits.

The PHE memo, seen by The Telegraph, warns of "quality assurance difficulties" in the programme, saying shortages of swabs and transport led to local variations in the way the national scheme has been run.

It says enzyme performance in the tests had degraded since the results were originally validated.

Health officials at PHE said on Tuesday that an issue was found in two labs towards the end of last month. They said staff had been given advice about how to "mitigate" the problems, with changes made to replace a component whose quality had deteriorated since the test begun.

An audit of 1,144 samples in one lab found 35 discrepant samples – a rate of around three per cent – compared with other firms, PHE said. Officials said after some changes were made this was brought down to less than two per cent.

Officials insisted the differencs did not mean the tests were worse than commercial tests, as either test could be incorrect.

PHE had previously boasted that it was one of the first in the world to develop a highly sensitive test to detect the virus and roll it out across the country. Health officials said the programme was always intended to move to commercial kits as soon as they were available, but set up the tests to ensure they could be made available more quickly.