Although the Prince paid for his own ticket to Canada, the cost of diverting at least one police protection officer to Toronto to guard him will be met by the taxpayer.
Whether Kensington Palace will be able to claim any refund on any pre-paid business class tickets back to London - also paid for with public money - was unclear.
The Prince's decision to visit Miss Markle, whom he had not seen for three weeks, defied the official Royal Household policy that members of the Royal family should not combine personal trips with official business.
In 2004, after the Duke of York had been criticised for combining official business with golfing breaks, the Royal Household assured the National Audit Office that such behaviour would stop.
The Royal Household said at the time: "Members of the Royal family are entitled to grant-in-aid for official travel, as are their staff and, where capacity permits, other officials.
"They meet their own costs, however, for private travel. In order to avoid confusion, combining private and public engagements in the same trip is actively discouraged."
The fact that the Prince has ignored official guidelines in order to spend a brief period with Miss Markle will only ramp up speculation that he may be considering proposing to the 35-year-old, who he has been dating since June.
The Prince, who left Guyana on Sunday after the final engagements of his two-week Caribbean tour, is thought to have returned to London on Monday as he has a commitment to help out at the City firm ICAP's 24th annual Charity Day today.
As the Caribbean tour came to a close, Miss Markle posted a photo on Instagram of her dog Guy wearing a knitted jumper with the British national flag on it.
Kensington Palace declined to comment.
