The 20-year-old stopper has played nine times for the first team this season, but was demoted back to Barca's second string last week.
Valdes, angry at being dropped, is backed by his agent Josep Maria Orobitg, who also believes that his client has been unfairly treated.
The pair believe that nobody at the Catalan club have given a good reason for the move and Valdes has threatened to stay away until someone explains why he has been relegated.
But Van Gaal and Barcelona are not happy and are preparing the maximum sanction in the club's doctrine.
"He has not turned up for training and I see that as a refusal to work," the Dutch coach explained. "The club now has to solve the problem.
"At Barcelona the technical director makes the final decisions in conjunction with the board of directors and the president, and they will have to see what to do."
The Blaugrana's team coach Quique Costas was shocked by the keeper's actions.
He said: "We expected to receive a phone call telling us that his car had broken down or something, but nobody rang and we have not spoken to him yet."
