Initial suspicions are that the pair, Fenix Two and Marching Song, were electrocuted, but authorities have stressed it was important that they probe all possible causes.
The Saturday deaths resulted in the cancellation of the race meeting. The first race went ahead, but the rest of the card was cancelled.
Some reports suggest underground cabling may be behind the deaths, but nothing has been confirmed.
Professor Tim Morris, director of equine science and welfare for the British Horseracing Authority, confirmed a full investigation was under way.
"Our sympathies go out to connections of the two horses that died, Fenix Two and Marching Song," he said.
"We have launched a full investigation into the events before the first race. Whilst there are suspicions that an electrical fault was the cause - and this is being looked into by the racecourse and relevant authorities - it is important that we investigate other possible causes."
Morris said both horses had been sent for post mortem examinations, and samples from both horses, and from the other two horses involved in the incident, have been taken and will be analysed.
"We will also be testing a sample of the water supply and have secured and will review all of the closed-circuit TV footage from the racecourse stables and footage from the parade ring itself at the time.
"We have gathered evidence and statements at the racecourse from the connections involved with the incident, including trainers, jockeys, stable staff and owners, the racecourse and British Horseracing Authority veterinary officers, and the racecourse executive including the health and safety officer."
A local report suggested people had been getting shocks off one of the horses before its death.