Williamson is intending to appeal a time penalty imposed on him which he believes cost him victory over the weekend.
The race was won by John Derry, of Blenheim, by 15sec from Williamson.
Williamson was looking in control for most of the weekend but in the second-last leg on the Matukituki River on Sunday he received a 1min time penalty.
Williamson was adjudged to have crossed the starting line too early.
The race started on the Clutha River on Friday and then switched to the Dart River at the end of Lake Wakatipu on Saturday.
The final legs of the race took place on the Matukituki River.
Williamson said it was a disappointing way to lose what had been an enjoyable weekend.
The high-powered boat he built last year had performed well and, on one leg on the Dart River, he had an average speed of 203kmh, which was seriously quick.
Derry had kept in touch but the time penalty had given him a real advantage as there was only one leg left after Williamson had his penalty imposed.
Williamson said yesterday he was unhappy and intended to file a protest.
He said the video evidence was inconclusive.
Drivers have a 10sec warning to get their boats up to speed before they cross the start line and Williamson had a dispute with how long the starting flag was up.
It was believed he was over the start line by about five boat-lengths, or about a second, Williamson said.
Williamson will put his case forward and then await the outcome.
Conditions over the weekend were great for jetboating.
The Dart River was a little discoloured while the Matukituki River was in fine condition.
The first leg - a lapped circuit from the Balclutha Bridge up river - was called off on Friday because of high winds but the weather cleared up after that.