McGrath, capped 83 times, was sent back to his club, Derby, with a damaged Achilles tendon as the rest of the Irish team left for Skopje. McCarthy said: "Everybody knows Paul's knees are in pieces. They are not going to get any better. They will get worse because whenever he trains he suffers.
"I wanted Paul here. He would have been involved in the game if he had been fit but in the end there was just no point in bringing him. But just because somebody is missing this time it doesn't mean he is going to miss the next game as well. And we have another big qualifier in Romania at the end of the month."
McGrath's latest setback came a couple of days after the Derby manager, Jim Smith, indicated he would not be offering him a new contract next season because of doubts over how long he can keep going with his famously "dodgy" knees.
"I've waited as long as I could because he is Paul McGrath but it didn't make the improvement I'd hoped for and we had to leave him behind," McCarthy said.
Aston Villa's Steve Staunton is struggling with a calf strain, although both he and McCarthy believe it will heal in time for him to play. Tony Cascarino had been rested from training after feeling tightness in a hamstring and the Norwich forward Keith O'Neill has pledged to give McCarthy his "best shot" despite having played just two games for his club since a long lay-off with ankle trouble.