The clash over the federation's move on Tuesday to exonerate Mourinho suggests the bad blood that has marred relations between the clubs in recent years is set to spill over into the 2012-13 season beginning next month.
"We are angry, we do not agree with the Spanish federation's decision," Barca spokesman Toni Freixa told a news conference after a board meeting in the Catalan capital on Wednesday.
"We believe that an aggression like Mourinho's should not go unpunished," Freixa said, adding that the Portuguese's actions were "treacherous", "very serious" and had been "witnessed by the whole world".
Barca believe the federation's decision, part of a general amnesty for sanctioned players and coaches, damages the image of Spanish football and can only encourage further aggression.
Mourinho, a former Barca assistant coach, was initially banned after attacking Vilanova, who has since taken over as first-team coach from Pep Guardiola, from behind during a Super Cup match last August.
His punishment was rescinded by football federation (RFEF) president Angel Maria Villar, who traditionally forgives some players and coaches after sealing re-election.
He was voted in unopposed for a seventh four-year term in February and his latest amnesty was announced at the RFEF's general assembly in Madrid on Tuesday.
Freixa said Barca had originally considered lodging a formal complaint against Mourinho but after consultation with players and coaching staff had decided to let the federation handle the case.
Now, after the lifting of the ban, the club had decided it wants a working group set up to examine the federation's disciplinary regime and Villar's amnesties, he added.
"Rules are needed that prevent cases like this from happening again, because this image being produced is very serious for Spanish football," Freixa said.
"We expect a positive response from the federation and if that is not forthcoming we'll have to look at other options. The legal course is open to everyone but it's not our basic plan."
The federation's decision meant Vilanova's one-match ban for reacting to Mourinho's aggression by pushing him away was also lifted, as were bans given to Real pair Mesut Ozil and Marcelo and Barca's David Villa, who were all red-carded.
All five are now clear to take part when La Liga champions Real and Copa del Rey winners Barca meet next month in the 2012 Super Cup, the two-legged curtain-raiser to the season.
The first leg is at Barca's Nou Camp stadium on August 23, with the return leg at Real's Bernabeu arena on August 30.