The Prime Minister was understood to have told his Cabinet on Thursday that the service should be cut by a fifth.
Mr Johnson made the demand during an away day with ministers in Stoke-on-Trent as his Government comes under intense pressure to ease the pain of soaring prices.
But the FDA civil servants union warned the “ill thought out” proposal would not lead to a more cost-effective Government and could have impacts on passport processing, borders and health.
Sources familiar with Mr Johnson’s Cabinet conversation said he told ministers to return the Civil Service to its 2016 levels in the coming years.
It was said its numbers have grown by 2016 since then to 475,000 full-time equivalent jobs.
The Prime Minister told the Daily Mail: “We have got to cut the cost of Government to reduce the cost of living.”
He suggested the billions saved could be used for tax cuts, saying: “Every pound the Government pre-empts from the taxpayer is money they can spend on their own priorities, on their own lives.”
Sources did not deny that the sweeping cut to public jobs could be used for future tax cuts.
Mr Johnson wants a recruitment freeze across Whitehall to start soon, with the abolition of any vacancies unless they are signed off by ministers.
Ministers are expected to report back within a month with plans for achieving the cuts from their departments.
FDA general secretary Dave Penman said the expansion of Whitehall since 2016 was necessary to “deal with the consequences of two unprecedented events – Brexit and the Covid pandemic”.
“To govern is to choose and ultimately this Government can decide to cut the civil service back to 2016 levels, but it will also then have to choose what the reduced civil service will no longer have the capacity to do. Will they affect passports, borders or health?” he said.
“Without an accompanying strategy, these cuts appear more like a continuation of the Government’s civil service culture wars, or even worse, ill-thought out, rushed job slashes that won’t lead to a more cost-effective government.”
A Labour Party spokesman said: “Instead of implementing an emergency budget they have chosen to let down working people once again through pointless rhetoric and lack of action.”
A Government spokeswoman said “the public rightly expect their Government to lead by example and run as efficiently as possible” as the nation faces rising costs.