Graham Ford, the judge who called an incorrect result at Lingfield on Wednesday, has been stood down from his duties while an investigation takes place.
Ford originally called Elementary as third in the seven-furlong nursery but was later forced to amend the result and name Sun Angel as third instead.
Some bookmakers paid out on both horses but they were under no obligation to do so, while some punters who backed the correct third, Sun Angel, were not paid out and vice versa.
Robin Mounsey, the British Horseracing Authority's media manager, said: "First, we wish to apologise to racegoers, bettors and bookmakers for an error in judging the 2.55pm race at Lingfield on Wednesday which led to the reversal of the third and fourth placed horses after the result had been declared for betting purposes.
"We take the matter very seriously and a full investigation is underway to understand the circumstances which led to the judge's initial error and to mitigate the risk of this happening in future.
"In the meantime, and pending completion of our investigation, the BHA can confirm that the judge concerned, Graham Ford, will not carry out the role of judge during this period.
"We accept that an error was made and acknowledge that the incident created confusion and frustration for both punters and bookmakers. It is a commercial decision for bookmakers if they wish to pay out on the amended result.
"From time to time, and for a variety of reasons, the result of a race is changed after the 'weighed in' announcement. In the circumstances, it would not be appropriate for the BHA to alter results for betting purposes, or to reimburse bookmakers or punters based on an amended result.
"Thankfully, events such as these are not common in our sport and our focus is on reducing the risk of them happening in the future."