Neymar only joined the Ligue 1 giants during the summer transfer window, and he has hit the ground running at the Parc des Princes with nine goals and seven assists from his 10 matches across all competitions so far.
The Brazilian has already been involved in a public dispute with teammate Edinson Cavani, and L'Equipe reports that he is now at loggerheads with Emery.
The row is understood to have stemmed from Neymar's desire to train for longer after Emery had ordered half of his players to end training early following Wednesday's Champions League clash with Anderlecht.
Neymar reportedly threw a ball at a wall in anger after Emery brought the training session to a premature end, causing a rift between the pair.
Emery's future at PSG has been called into question amid growing speculation that the club are eyeing up Jose Mourinho as their next manager.