Valdes will not be travelling with his team to their weekend fixture, leaving his future within the club's setup unclear.
At the present moment, the former goalkeeper's future with Juvenile A is hanging by a threat, with the club releasing a statement on Friday evening.
"Although they haven't yet publicised the reasons for the disagreement, Valdes has already informed his players that he doesn't know if he'll remain in the job," a reporter explained on Catalunya Radio's Tot Costa program.
The root of the controversy surrounds a disagreement with Patrick Kluivert, the club's academy director, and a decision by the club is expected to be formalised in the coming days.
Valdes was upset with Barcelona's hierarchy for how few opportunities his team was getting to play at the Estadio Johan Cruyff within the Joan Gamper Sports City complex.
"I thought that such a beautiful stadium would be ours, but it's not like that," Valdes explained.