The 18-year-old 'Baby' hitmaker, who previously scored two nods at the 2011 ceremony, was omitted from the 2013 nominations list which has fun., Frank Ocean and The Black Keys leading the pack, reported TMZ online.
Bieber's manager, Scooter Braun, was furious when it became clear the singer had not been recognised and blasted organisers in a series of angry messages on Twitter, saying, "Grammy board you blew it on this one. The hardest thing to do is transition, keep the train moving.
"The kid delivered. Huge successful album, sold out tour, and won people over... This time he deserved to be recognised," he said.
Cowell has now waded into the debate and called Grammy bosses out for shunning Bieber.
"You know what? He deserved one (a nomination), I think. But they can get a bit snobby sometimes."
However, Cowell is convinced Bieber won't be too worried about the snub, adding, "He won't be crying too much. He's doing fine," he added.
The Grammy Awards will be handed out in Los Angeles on 10 February 10.