Balotelli lasted only 13 minutes of today's test match with Italy's Under-18 side when he limped off with a right knee problem.
"Balotelli suffered a relapse of the pain in the right knee that had already troubled him in the past," explained Professor Enrico Castellacci.
"It was a small sprain of the right knee. It'll be difficult to get him back by Friday, so he's unlikely to recover in time to face Estonia.
"Between today and tomorrow we will evaluate whether to keep him in the squad or send him home."