The confrontations took place outside the Vicente Calderon prior to Sunday's La Liga encounter and resulted in the death of a Deportivo fan Francisco Javier Romero Taboada.
Atletico have already moved to ban a number of supporters as well as the Frente Atletico fan group, with both clubs and the Spanish Football Association (RFEF) condemning the violence.
Fernandez has since gone on to state his intention to ban the 'Riazor Blues' group from Depor's ground, stating the closure of a section of the Riazor was the first step.
"I am certain that we will not have any more Riazor Blues at the Riazor," he told Spanish radio station Onda Cero.
"The first step we have taken is to close the Riazor Blues section of the stadium for our next two home games.
"This is the first measure as there is still an investigation going on.
"We don't have to act against an organisation because the Riazor Blues are not registered as a fan club.
"We have to act against people and we are not sure who those are just yet."
