John Parker, the former chairman of the Royal College of Veterinary Surgeons, said the owner of Spindles Farm in Hyde Heath was “not aware of the gravity” of an infection affecting his livestock.
But he also told Bicester Magistrates' Court he was unable to prove his theory as it was several months before the idea came to him.
Mr Parker said he believed the horses could have died from a condition called cyathostomiasis – an infestation of worms.
Robert Seabrook QC, prosecuting, suggested it was “impossible” for so many animals to die in such a short space of time.
He asked Mr Parker: “Can you have sudden death from acute cyathostomiasis without a preceding tell tale disability – clinical signs that would be apparent to the keeper?”
Mr Parker said this was possible, adding they could have died within 48 hours of contracting the disease.
He said if this was the case it would be “one of the largest outbreaks ever recorded” if properly documented.
But he added: “I am giving the hypothesis that's what killed the animals, but we cannot prove that because unfortunately evidence has gone.”
Mr Parker said the possibility of cyathostomiasis did not cross his mind until after he had compiled his initial report on his findings.
Mr Seabrook suggested Mr Parker “did not have any personal knowledge or experience” of cyathostomiasis.
The vet disagreed, but added he “did not know what yardstick” to measure his findings against. He said he had seen two outbreaks of the condition.
Mr Seabrook said Mr Parker had been “swotting up” on his knowledge of the disease and he had contacted another vet from Shrewsbury to ask about it.
Mr Parker agreed he sought advice from the vet: “I sought his confirmation whether his experience of sudden death was the same as mine, which was so.”
He said he had spoken to him “three or four times”, but added they were good friends and he had never contacted him specifically with the intention of talking about the trial.
Mr Parker told the court evidence from vets and RSPCA inspectors heard already had been “exaggerated” and “overstated”.
He looked at photographs taken by the RSPCA at the farm, owned by 45-year-old James Gray.
Referring to evidence from vet Katie Robinson, Mr Parker told the court: “Neglect and cruelty may well not have contributed to everything that she saw.
“I realised whatever happened there may be outside Mr Gray's control. Unfortunately, although he wormed his horses, he didn't know the gravity and complexity of the potential situation.”
Mr Seabrook asked the vet if he would be “cautious” about challenging Miss Robinson's evidence.
Mr Parker said he would not, but added he did not contest her remarks the animals were “in urgent need of attention”, that people “normally asked for help” before horses ended up in the condition they were found and they would die unless they received attention.
He said: “If Mr Gray was a reasonable dealer he would give them enough food to keep their weight up over the winter, but not to put a great deal of flesh on them.”
Mr Seabrook said Mr Parker had not mentioned cyathostomiasis anywhere in his report on the findings – which amounted to 73 pages.
The vet replied: “My remit until April 4 was not to do with diagnosis. It was to see some horses and see how healthy they were.”