The plane used by Boris Johnson and members of the royal family for international travel is being repainted in the colours of the Union flag to "better represent" the UK abroad.
The red, white and blue "rebranding" will cost about £900,000, No 10 said.
Downing Street said it represented "value for money" and that all of the work was being done in the UK.
But opposition parties were critical, saying the money would be better spent on helping the victims of coronavirus.
No 10 said the aircraft was currently in Cambridgeshire for pre-planned repainting in "national branding".
Asked about the plane at the daily coronavirus press briefing, Culture Secretary Oliver Dowden said "we have always spent money on promoting the UK round the world" and added that the work on RAF Voyager was part of that effort.
The RAF Voyager is used by the prime minister, other ministers and senior members of the Royal Family for official engagements.
It said the makeover would mean the plane "can better represent the UK around the world, while also maintaining its military air to air refuelling capacity".
Downing Street said all of the work was benefiting UK suppliers.
Marshall Aerospace and Defence Group told the BBC they are carrying out work on the aircraft, which is much bigger than ones they would usually work on.
But acting Lib Dem leader Sir Ed Davey said the money would have been better spent on supporting treatments for coronavirus patients.
The drug dexamethasone, that can potentially save the lives of people with coronavirus, costs £5 per patient. @BorisJohnson could have bought 180,000 doses of that, but instead he's painting a flag on a plane. https://t.co/PJvhVNtS2n— Ed Davey MP 🔶🇪🇺 #StayHomeSaveLives #ProtectNHS (@EdwardJDavey) June 17, 2020
And the SNP hit out at the timing of the move, which follows Tuesday's u-turn by the government over providing school meal vouchers for low-income families over the summer holidays.
PM won’t find an extra £20 a week to support the most vulnerable in society and help parents feed their children in these difficult times.— The SNP (@theSNP) June 17, 2020
But he can find almost a million pounds to paint a plane.
Westminster is broken. Surely we can do better. pic.twitter.com/wiXJWcER2E
Labour questioned why the government was spending nearly a million pounds "redecorating a plane which in all likelihood has been grounded for months because of the coronavirus".
"When families across the country are worried about their jobs, health and the education of their children, they will rightly question the government's priorities," said shadow Northern Ireland secretary Louise Haigh.
And Labour MP Chris Bryant told the BBC it was "just a vanity project for the prime minister".
"People who are on furlough in my constituency and are terrified they are going to lose their jobs will be wondering why on earth this is a priority," he said.
The RAF Voyager, an Airbus A330 jet, was re-purposed for use by the UK government in 2015, at a cost of £10m.
It was first used to take David Cameron and other ministers to the Nato summit in Poland in July 2016.
At the time, the government defended the expenditure, saying it was cheaper than chartering flights and would save about £775,000 a year.