The BBC reported that one ex-civil servant refused to pay to cover the costs of a massage for the former prince, but was overruled by senior staff, telling the broadcaster: "I thought it was wrong ... I'd said we mustn't pay it, but we ended up paying it anyway."
A former government official, who oversaw finances, separately told the BBC they had "absolutely no doubt" about the authenticity of the claim after having seen similar expenses for his overseas trips.
Their words come as police searches of Andrew's former home, Royal Lodge in Windsor, Berkshire, were expected to continue into Monday following his arrest on suspicion of misconduct in public office on Thursday.
The former prince spent 11 hours in custody on his 66th birthday while officers searched his home on the Sandringham Estate in Norfolk before he was released under investigation.
Andrew is accused of sharing sensitive information with convicted sex offender Jeffrey Epstein during his time as UK's special representative for international trade and investment.
In a videotaped interview under oath in 2009, Epstein's former Florida housekeeper Juan Alessi said Andrew would have "daily massages" when he visited.
Speaking about the alleged use of taxpayers' money for massages during his time as the UK's trade envoy, the whistleblower who spoke to the BBC said: "I can't say it would have stopped him, but we should have flagged that something was wrong."
A separate civil service official, who said Andrew claimed for excessive flights, hotel rooms and charges for his entourage, told the broadcaster: "I couldn't believe it... it was like it wasn't real money, they weren't spending any of their own money."
Calls have grown from a range of public figures for a wider probe into Andrew's past dealings with disgraced financier Epstein.
He has denied any wrongdoing over his links to the convicted sex offender, but has not directly responded to the latest allegations.
Despite being stripped of his title in 2025, the former duke of York is still eighth in line to the throne, and an act of parliament would be required to remove Andrew and prevent him ever becoming king.
Prime Minister Keir Starmer's government will consider introducing such legislation once police have finished their investigation into the King's disgraced brother, the Press Association understands.
On Sunday, the Prince and Princess of Wales made their first joint public appearance since the arrest, attending the BAFTA awards on Sunday evening.
During the event, William told Elaine Bedell, chief executive of the Southbank Centre, and Allison Kirkby, chief executive of BT Group, that he had yet to see Hamnet - adding: "I need to be in quite a calm state and I'm not at the moment."
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