The Office of the Scottish Charity Regulator has confirmed it is investigating Havisham's decision to buy up the unwanted properties in Knockroon.
A spokesman said: "We can confirm that the work of Havisham Group and property transactions relating to the Knockroon development in Ayrshire forms part of our overall investigation, work on which is ongoing."
Lord Brownlow, whose wealth is estimated at £271 million, hit the headlines last year when it emerged he had helped fund the refurbishment of Boris Johnson's Downing Street flat.
He was also recently reported to have been linked with plans to potentially fund a £150,000 treehouse for the Prime Minister's son.
In 2012 Lord Brownlow's property company began bailing out the Knockroon development by buying up some of the unwanted houses and converting them into buy-to-lets and a cafe.
The eco-village, built on farmland bought by the Prince when he purchased Dumfries House, had been intended to boost the local economy by championing sustainable architecture and attracting people to the area.
But by 2015, Hope Homes, the developer working with the Prince's Foundation, had withdrawn from the project and plans to complete all 770 properties have now been abandoned.
Havisham Properties is understood to have spent £1.7 million buying up 11 houses on the site, while other properties were purchased on behalf of Dumfries House and are now let out to staff who work at the nearby estate.
Sales not declared as 'related party transactions'
The Prince's Foundation did not declare any of the sales as "related party transactions", which is a standard procedure intended to demonstrate that the trustees knew the deals involved someone with existing links to the charity.
In 2013 - two years after Havisham Properties began buying houses in Knockroon - Lord Brownlow hosted a lavish 50th birthday party at Dumfries House, which is available to hire when the Prince is not resident.
In 2015 Lord Brownlow's companies were awarded a £1.2 million contract to build three cottages at Dumfries House.
And in 2018, after resigning as a trustee at the Prince's Foundation, Lord Brownlow was a guest at Buckingham Palace where he received a CVO and honour which is conferred for extraordinary, important or personal services to the Royal family.
A spokesman for the Prince's Foundation said: "Lord Brownlow was appointed CVO in 2018 in recognition of his role of chairman of the charity The Prince's Foundation for Building Community."
Lord Brownlow's own charitable foundation has donated millions to a variety of worthy causes including Macmillan Cancer Support and the National Association for the Children of Alcoholics.