It comes as the prime minister used a national address on Sunday, in which he urged all adults to get booster jabs.
According to the UKHSA, fewer than one in 10 PCR tests from Westminster, Kensington and Chelsea and the City of London were sent to labs which tested for the S-gene dropout from July 1 to November 28, 2021.
Westminster sent just 8.6% of PCR swabs to these labs, while Kensington and Chelsea sent 9.4% and the City of London sent 9.7%.
This compares to just under four in ten, or between 30-40%, from Bexley, Greenwich and Lewisham.
Bexley sent 38.3%, Greenwich sent 33.1% and Lewisham sent 31.8%.
See what the situation is like in your area with our interactive map.
About one in every six positive PCR tests are sent for genome sequencing to determine which variant they are - a process which can take many days.
A quicker way to spot potential Omicron cases is to look for a marker called the S-gene, which is missing in variants such as Omicron and Alpha but present in Delta cases.
Once identified, swabs showing so-called ‘S-gene dropout’ can then be sent for definitive testing for Omicron.
Four UK labs use a Covid testing system which detects the S-gene - at Newcastle, Milton Keynes, Glasgow and Alderley Park in Cheshire.
But only about a third of PCR swabs are sent to one of these sites, rather than other labs, with the proportion varying widely across the country.
Use of these labs is low in central London, leading to fears hotspots are going undetected.
Prof Rowland Kao, of the University of Edinburgh, who contributes to the Scientific Pandemic Influenza Group on Modelling (Spi-M) government advisory group, said geographical patchiness of S-gene dropout testing was a concern.
He said: “If we want to slow down the spread of Omicron in the UK, we need to be able to identify geographical clusters”.
Health secretary Sajid Javid has told the House of Commons labs have now brought in other methods to try to detect the new variant, and the capability is being expanded.
A government spokesperson said: “All samples from international arrivals to the UK, contacts of suspected and confirmed cases will have their samples analysed by labs that can detect suspected Omicron cases.
“These samples will be sent for sequencing to confirm the initial results.
“We are constantly reviewing our laboratory testing capacity and capability to ensure that the COVID-19 testing programme is as effective as possible.”