Adelaide trainer Phillip Stokes has scratched two horses from Flemington and one from Morphettville amid concerns after a security breach at his stable.

There was evidence an intruder had entered his stable on Wednesday night and Stokes decided to err on the side of caution ahead of Saturday's racing.

His two Flemington runners, Counterplay and Trogir, were due to leave for Melbourne on Thursday night and Stokes also scratched Eclair Attack from his race at Morphettville.

Gravitational, who was stabled away from the other three horses, is likely to take his place at Morphettville.

Stokes, who is sitting second on the Adelaide metropolitan trainers' premiership, Stokes said he didn't want to take the risk of running the three horses.

"I was worried enough to scratch the two horses from Melbourne due to not knowing if they were drug-free," Stokes said.

"The horses appear fine but we don't know if they've been given anything."

Stokes said Thoroughbred Racing South Australia stewards had taken blood samples from his horses on Friday morning.

He said stewards were conducting inquiries as there had also been a later breach at a different stable which he said had concerned trainers in the Morphettville area.

Stokes says he is now considering installing CCTV in his stables.

Before the incident he believed he had one of the most secure stables in Adelaide.

"If someone really wants to get in, locks won't stop them," Stokes said.

"Hopefully the stewards will get to the bottom of it."