The Galileo colt, winner of the Irish Derby and St Leger last season, made a winning return at Naas last month, but is now likely to miss the Coronation Cup at Epsom.
"Capri had a little setback after his run at Naas," said O'Brien.
"He bruised a shoulder and is just not 100 per cent yet. So I wouldn't say he will make Epsom (Coronation Cup)."
In other O'Brien news, Saxon Warrior has been given a clean bill of health following his Qipco 2000 Guineas success at Newmarket and will head for the Investec Derby.
Several other Ballydoyle colts will put their Epsom claims on the line this week.
O'Brien said: "The lads are thinking of the Derby for Saxon Warrior. The Pentagon, Nelson and Delano Roosevelt will all go for the Derrinstown (Derby Trial at Leopardstown)."
O'Brien will saddle a handful of runners for the trials at Chester this week, while York's Dante Stakes could also come into the equation.
"Rostropovich and Kenya will go up to a mile and a quarter at Chester. Kew Gardens will go to Lingfield. Depending on the weather, some of the horses heading to Leopardstown could go for the Dante," said O'Brien.
As for his fillies, it appears the Ballydoyle handler will have a very strong hand in the Irish Guineas.
"Happily will probably go for the Irish Guineas next. September is on the way back and you would hope she will make the Oaks, but she is not guaranteed," he said.
"Magical is looking at the Irish Guineas at the moment and if she wasn't to go there she could go straight to the Oaks.
"Clemmie is good and she is going to run in the Irish Guineas. She will be just ready to run, so whatever she does there she will step up a lot. The plan is to go from there to Ascot.
"Flattering will go to Lingfield for the Oaks Trial, and Could It Be Love goes for the French Guineas. U S Navy Flag goes for the French Guineas as well."
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