The veteran Italian faces the daunting task of having to take something from reigning World and European champions Spain in Gdansk on Thursday evening if his side are to prolong their interest in the tournament.
Trapattoni, who saw his strongest available team defeated 3-1 by Croatia in Poznan, could now opt to shuffle his pack and has urged his players not to be too disheartened if they miss out.
He said: "It's early now. I know you want to know what happens, but we have to think about how the players are with fitness.
"Spain is another game and then we have to think very, very much.
"If I decide to change, it will not be because a player played badly or does not deserve to play. We have another game. Our opponent only drew and has only one point.
"It's important we recover psychologically and believe again because we have to remember how many games we had played without conceding a goal."
The Republic were undone by impressive Croatia striker Mario Mandzukic within three minutes, and although defender Sean St Ledger dragged them back into the game with a 19th-minute equaliser, they fell behind once again two minutes before the break.
Everton striker Nikica Jelavic made the most of Stephen Ward's miskick and a tight offside decision to make it 2-1 and, when Mandzukic's 48th-minute header came back off the woodwork and went in off keeper Shay Given, the die was cast.
Trapattoni said: "In the first half, they deserved to win because they were superior in midfield. We played better in the second half."
Croatia boss Slaven Bilic was delighted, but not surprised, by his side's powerful display, which sends them into their clash with Italy brimming with confidence.
Bilic said: "I was expecting this kind of result. We were preparing for this victory. We knew everything about this Irish team.
"We knew we were the better team, but you never know before the match. I can just congratulate players from both teams. The match was very good.
"I respect the Irish team. The Irish team didn't lose for the last 14 matches, they were in a group with Russia, they drew 0-0 in Moscow - this means they are a strong team.
"We played very well and we beat a strong team.
"We were dreaming about this position. Probably, one victory will be enough to go to the quarter-finals."