The 31-year-old defender aggravated a calf injury late in the first half of this afternoon's 1-0 Barclays Premier League defeat by Manchester United, and O'Neill later admitted he could be a doubt for Poland and Ukraine.
He said: "John didn't feel comfortable. He has come back and he was starting to feel his injury, so he just didn't feel confident at all about moving on it."
Asked if that could jeopardise his chances of representing the Republic this summer, O'Neill added: "It might do.
"As he came off, that was my thought, that there might be a concern about it.
"I haven't had a chance to check with the physios since that. Maybe I am jumping the gun, but it might be a concern."
That would come as a huge blow to Ireland boss Giovanni Trapattoni, who has been able to count upon O'Shea as one of his most dependable performers during his four years at the helm.
O'Shea and the rest of Trapattoni's Premier League-based players are due to meet up in Malahide next Sunday to begin their preparations for the tournament.
However, the Italian now faces an anxious wait to discover whether the defender will be there and indeed, whether he will be fit for the opening game against Croatia in Poznan on June 10.
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