Central defender Sean St Ledger picked up a hamstring injury during Leicester's 2-0 npower Championship victory over Bristol City on Saturday, while winger James McClean reported a tightness in his groin following Sunderland's 3-0 Barclays Premier League defeat at Manchester City.
St Ledger will join up with the rest of the squad on Monday to have his injury assessed, but McClean will remain on Wearside for a scan.
A spokesman for the Football Association of Ireland said: "Sean St Ledger sustained a suspected hamstring injury. At the moment it looks unlikely that he will be able to play in the Germany match, but he will report for assessment.
"James McClean reported a very tight groin after his match and will be scanned at his club on Monday."
The news will come as a fresh blow to Trapattoni, who has already lost striker Kevin Doyle to a thigh problem.
Manchester United winger Robbie Brady, who was initially placed on the stand-by list, has already been drafted into the squad along with Sunderland's David Meyler, and it remains to be seen if the Italian calls for further reinforcements.
Ireland face Group C favourites Germany at the Aviva Stadium on Friday evening and then head for Torshavn for the clash with the Faroes next Tuesday.
They launched their qualification campaign with an unconvincing 2-1 win in Kazakhstan last month and will be looking for a significant improvement this time around.