In a reply to a written question from SNP MP Neil Gray, work and pensions junior minister Will Quince confirmed benefits claimants would see the payment considered as additional earnings, with benefits reduced accordingly.
It follows an early move from the SNP to call on the UK Government to cancel tax on the payment, something the respected economics research unit the Fraser of Allander Institute said was in the power of the Scottish Government to avoid.
It is also not clear how many NHS workers in Scotland this would affect.
Universal Credit rules state that for every £1 in additional earnings, 63p is removed from the monthly payment of Universal Credit – a policy known as the ‘taper’.
The DWP claim the same rules would have applied in legacy benefits, while the Scottish Conservatives criticised the SNP for using NHS workers as “political pawns”.
Mr Gray, the SNP’s shadow work and pensions secretary, said: "The Tory government must U-turn on its plans to cut benefits for NHS and social care workers receiving the Scottish Government's £500 'thank you' payment.
"This payment is in recognition of the extraordinary role frontline workers have played in tackling coronavirus - and it should be received in full without UK Government deductions.
"After a decade of Tory austerity cuts, which have pushed millions of people into poverty, it is shocking that the Tory government is now planning further cuts, including a public sector pay freeze, which will leave so many frontline workers poorer and worse off.
"Instead of taking money away from our NHS and care workers, the Tory government should follow Scotland's lead and ensure workers across the UK get the recognition they deserve.
"Scotland shouldn't have to wait for Westminster to act. The whole sorry saga demonstrates, yet again, that the only way to properly protect Scotland's interests is to become an independent country - with the full powers to make our own decisions and build a fairer country."
A Scottish Conservative spokesman criticised the use of NHS workers as “political pawns” by the SNP.
They said: “Using NHS staff as political pawns backfired on the SNP, but they’re already at it again.
“As the Fraser of Allander Institute made clear last week, the SNP are playing political games with this thank you payment.
“The SNP lack the same spiel about independence at the end of every press release and this one is exactly the same. They don’t even try to hide it, it’s right there in black and white that this is all just about independence for them and treating NHS workers as political pawns is fair game if it achieves their goal.”
A Department of Work and Pensions spokesperson said: “We recognise the absolutely vital role that all key workers continue to play.
“The rules here apply to all workers’ bonuses, which are treated as earnings and just as under the legacy benefit system, claimants would not have kept all of their bonus.”