The two scientific experts leading the response to the coronavirus pandemic earn almost £400,000 between them.
Chief medical officer Professor Chris Whitty is paid between £205,000 and £210,000 while chief scientific adviser Sir Patrick Vallance is on up to £185,000.
Thirty officials at soon-to-be scrapped Public Health England earn more than £150,000.
The agency’s former chief executive Duncan Selbie still gets up to £195,000 as a senior adviser to the Department of Health. He received a £5,000 pay rise before losing his job.
Meanwhile, seven staff at NHS Test and Trace, which has been blasted for its ‘shambolic’ performance, earn more than the Prime Minister.
Professor Whitty and Sir Patrick appear on the list of best-paid civil servants for the first time.
The list revealed that four PHE staff are on salaries of more than £200,000.
In Prof Whitty this is because he is newly-appointed to the role. His predecessor Dame Sally Davies actually earned £5,000 more than him the previous year.
Read more: Top scientific advisers rake in £400k: Chris Whitty and Patrick Vallance are earning a fortune during Covid-19 pandemic and have appeared on the list of best-paid civil servants for the first time