The striker aggravated a muscular tear in the national team's 2-0 win over Andorra last Friday.
Keane suffered further damage when he pulled the ball back for Kevin Doyle's opening goal in the seventh minute, but went on to complete the full 90 minutes.
The 31-year-old missed the 2-1 win over Armenia on Tuesday as a result and there are fears that Keane could miss next month's Euro 2012 play-off matches.
"If it was a knock, I am not afraid but he made it worse [by playing on]," said Trapattoni.
"I said to him that he should have said immediately and maybe go off. It should be immediately with muscle [problems]. Never discuss, never put into question the muscular problems.
"He was a doubt before the game with it. Sure, you can never play 90 minutes with this injury."
The first leg of the Euro 2012 play-off matches are scheduled for November 11 or 12, with the return leg due to be played on Tuesday, November 15.