In areas where relatively few people are being tested, the programme is being used to provide an early warning for local outbreaks.
The government-led scheme, which was first announced in June, is successfully detecting fragments of genetic material from the virus in waste water.
Data from this testing, which has been rolled out to more than 90 waste water treatment sites across the UK, is being shared with the Joint Biosecurity Centre as part of NHS Test and Trace.
It comes as Boris Johnson admitted the coronavirus test and trace system needs to improve, as the system recorded its worst ever week.
Just 59.6% of close contacts of people who tested positive for Covid-19 in England were reached through the system in the week ending October 14.
Defra said fragments of the coronavirus are passed out from people’s bodies when they use the toilet. The detection of the material, which is not infectious, can indicate when a local community is having a spike in cases.
Officials said the results of testing can give local health teams a clearer idea of infection rates by identifying where there are high numbers, particularly of asymptomatic carriers and people before they start showing symptoms.
This can help them take early action to slow the spread of the virus.
Defra said the project had already worked successfully in an area of the south west of England, where sewage sampling showed a spike in coronavirus material despite relatively few people getting tested.
The information was passed on to NHS Test and Trace and the local council who were able to alert local health professionals to the increased risk and contact people in the area to warn of the rise in cases.
Environment Secretary George Eustice said: “This is a significant step forward in giving us a clearer idea of infection rates both nationally and locally, particularly in areas where there may be large numbers of people who aren’t showing any symptoms and therefore aren’t seeking tests.
There are currently 44 sites in England where sampling is being done, covering 22% of the population, with plans to roll it out further.
There are also 24 sites in Wales and 28 in Scotland where sampling is being done, with the projects being led by the devolved administrations and the UK government coordinating the findings.
Health Secretary Matt Hancock said: “This initiative is just one example of how we are working across government and with local partners to find innovative, new ways to track the outbreak, slow the spread of the virus and save lives.
“Monitoring and sampling wastewater offers another tool to help us identify outbreaks early on – helping NHS Test and Trace and local authorities target hotspots quickly and effectively.”
Separate work carried out by the National Institute for Biological Standards and Control (NIBSC) also identified coronavirus material in London sewage in February, before cases were recorded in the area.
High levels of virus material were detected in March and April, followed by a considerable decrease in May and June, reflecting how the national lockdown curbed virus transmission.