Javier Tebas has implied that Barcelona players provoked Valencia supporters during the Catalan side's dramatic 3-2 win at the Mestalla at the weekend.
A bottle was thrown on to the pitch at Mestalla as Barca celebrated Lionel Messi's stoppage time winner from the penalty spot in front of the home supporters.
Neymar and Luis Suarez were both hit by objects and fell to the pitch, leading Messi to confront the fans and pump his fist.
La Liga president Tebas said that the fact that objects were thrown in the direction of Messi, Neymar and Suarez makes the incident a serious matter which needs dealing with.
However, he said that Barca players were not without blame on Saturday.
"You have to go in order and the first and most serious thing is the bottle [incident]," he said at La Liga's awards night on Monday.
"That's the most serious thing which occurred, but some of the conduct from some of the players is not what I like [to see]."
When pressed on specifics, he wouldn't it narrow it down to a particular incident.
He limited his comments to: "What happened at the end I did not like."
Valencia have reportedly said that Neymar's actions after the Messi goal provoked the anger among the Valencia fans.
"Neymar was wrong to taunt the crowd," Valencia midfielder Dani Parejo told LaSexta. "The fan was wrong to throw the bottle, but so was Neymar.
"It's a difficult moment and not the time to provoke people. You may be happy because you're taking three points home with you, but do not think you have to antagonise others."
Tebas, who's never hidden that he's a Real Madrid fan, denied any bias in his judging of the events and insisted that everyone playing in Spanish football needs to behave with more respect, regardless of who they play for.
"A few years ago I condemned Cristiano Ronaldo's actions towards a referee, too," he said. "What the players must try to do is to maintain their sportsmanship at all times."
Barcelona president Josep Maria Bartomeu, meanwhile, defended the right of his players to celebrate what was a big goal at the end of an intense fixture.
"I think it was a competitive game," he told reporters. "The players celebrated the goal with the expected exuberance. I think when you win a game, celebrations [like that] are logical."
Bartomeu was also speaking at the LFP gala, where Luis Suarez and Lionel Messi were given awards for being La Liga's top scorer and best forward last season, respectively.
Neither of the players were present at the event, though, something which also irked Tebas.
"I would have liked it if some players from Barcelona had been here and if they could have been here perhaps it's a lack of respect [that they're not]," he said.
Elsewhere on the night, there were a number of prizes for Atletico Madrid, with Antoine Griezmann winning the best player award in the Spanish league for last season.
Diego Simeone won the best coach award, Diego Godin earned the best defender tag and Jan Oblak clinched best goalkeeper. Real Madrid's Luka Modric was named best midfielder.
On Satuday, new Valencia coach Cesare Prandelli hinted more than once after Saturday's game that referees have too much respect for the top teams.
"Everyone knows that the big teams always have a `psychological advantage,' as we say in Italy," Prandelli said. "It's the same in every country."
Valencia fans loudly complained about calls against Prandelli's team, including the last-minute penalty after Aymen Abdennour fouled Suarez inside the area and a non-call of an alleged penalty on striker Rodrigo about 10 minutes later.
They also argued that Sergio Busquets should have received his second yellow card for a hard foul just before halftime.