Heskey played the first half of England's 2-0 international friendly defeat to Spain in Seville on Wednesday, despite picking up an Achilles injury during Villa's victory at Blackburn Rovers last weekend.
O'Neill is set to speak with England boss Fabio Capello after striker Heskey aggravated the problem and is now a major doubt for Sunday's FA Cup clash with Everton at Goodison Park.
He said: "Emile has aggravated his Achilles. I was surprised he started the England game. He had come off against Blackburn last weekend.
Assessed"The ruling now is that you go down and be assessed at international level by the international medical team.
"Knowing Emile, he would have wanted to have gone down there and played in a bit of discomfort but I was surprised he played considering he wouldn't have been fully fit.
"I didn't speak to Fabio Capello beforehand. I would have thought those things would have been pretty straightforward.
Sore"Emile has come back, he didn't train today, the Achilles is particularly sore at this minute. If the game was this minute, he couldn't play.
"It was a friendly international at the end of it all. I can understand it if it was a qualifying game because they are very important to the well-being of the country.
"But you would have thought rest this particular week would have been the order of the day. I have spoken to the England doctor and voiced some concerns and I will speak to the manager."