The defender hit out at the Portuguese, who was seen to poke Barca assistant boss Tito Vilanova in the eye following the sides' bitter Supercopa clash at Camp Nou
Barca won an entertaining match 3-2 thanks to Lionel Messi's late winner, his second goal of the night after also laying on the first Barca strike for team-mate Andres Iniesta.
Karim Benzema and Cristiano Ronaldo had responded for Madrid, but it was another Portuguese, Mourinho, who will make the headlines after he poked Barca assistant coach Tito Vilanova in the eye following a brawl at the end of the match.
"I hope the brawl isn't what is talked about - it's a shame," Pique told reporters after the match. "It's not the first time it has happened and it's always the same players.
"Someone has to take action here - Mourinho is destroying Spanish football. They talk a lot about the Catalans, but the problem is in Madrid."
Barcelona coach Pep Guardiola was also left frustrated by Mourinho's antics, and Pique believes the Portuguese has gone too far.
"I think he is crossing the line and the limit, and he needs to be stopped," he said. "We can't end up like this every time. If we do, things will get worse."