He was taken to Phuket International Hospital, where he is listed in stable condition. A police guard has been mounted for his protection.
Police are keeping certain aspects of the case under wraps, but said that Mr Danunan was on his way to a meeting with "business partners", carrying B400,000 with him in the car.
He was shot from a motorbike through the side window of his car and the money was stolen.
Mr Danunan identified the gunman, whom he knew, though police have named him only as "Man".
Police arrested Man on Friday and were questioning him about the reasons behind the shooting.