The Duke of Rothesay has garnered support from both the NHS and local authorities for the centre, which will primarily cater for patients with conditions including obesity and cancer.
The new centre will be built at Dumfries House, the stately mansion in Ayrshire that the Prince bought in 2007.
As well as complementary therapies, fitness and education programmes will also be on offer.
While Dumfries House has mainly been used as a visitor attraction and community centre, the Duke has also used it to showcase causes close to his heart, including traditional craft, according to The Times newspaper.
The cost of constructing the centre will be funded by private donations. Running costs will be met using profits made from Dumfries House.
Kenneth Dunsmuir, deputy executive director at Dumfries House, said the whole estate was a ‘realisation of the prince’s vision’, adding: “There are so many different things he champions and here he can make them happen.”
Prince Charles has been a long-time advocate of alternative medicine, calling for the NHS to recognise the ‘core human elements of mind, body and spirit’ while the 2015 publication of the ‘black spider memos’ revealed that he had lobbied the last Labour government to concentrate public spending plans on complementary medicine.