Trapattoni told a news conference that Sunderland winger McClean, who has a hip flexor strain, will almost certainly be ruled out of the Germany clash on Friday and may also miss the Faroe Islands game on October 16.
The other two, who like McClean were part of Ireland's Euro 2012 squad, will undergo scans later before a final decision is made but it is highly unlikely they will play on Friday.
Ciaran Clark has therefore been called up to the squad.
Central defender Mats Hummels has been replaced in Germany's squad by Heiko Westermann of Hamburg SV for the against Ireland on Friday and Sweden four days later.
Hummels is iout for two weeks after he hurt his leg in Sunday's 1-1 Bundesliga draw against Hanover.
Westermann has not played for his country since the goalless draw with Sweden in November 2010.