Barcelona president Josep Maria Bartomeu said on Tuesday the club had terminated its contract with PR company, I3 Ventures, who had been hired to improve the image of Bartomeu and the club's board online.
According to Spanish radio station Cadena Ser Catalunya, the company oversaw “dozens” of accounts attacking the likes of Messi, Gerard Pique, Xavi Hernandez, Pep Guardiola and Carles Puyol on Facebook and Twitter.
Among the messages the report cited is one expressing anger towards Messi for his delay in signing a new contract and another questioning Pique's involvement in tennis' Davis Cup.
“The truth is that I find it strange that something like this happens,” Messi said in an interview to be published on Thursday by Catalan newspaper Mundo Deportivo.
“But they also said that there would be evidence. We will have to wait to see if it is true or not. We cannot say much and wait to see what happens with all this. It seems a strange issue,” added the Barca captain.
Bartomeu has met with senior players, including Messi, to explain the case.
“The president told us the same thing he said publicly, the same thing he said at the press conference. What was the situation, what had happened. I can't say much more,” Messi said.
In a statement on Monday, Barcelona denied that it was behind the messages and Bartomeu reiterated that stance on Tuesday.
“Barca has never hired a service to discredit anyone,” he said. “Not a player, not a former player, nor any politician, manager, president or former president.”
Bartomeu added: “That is flatly false. We will defend ourselves where necessary on this issue, by all means.”
Barcelona had already threatened legal action against any media organisations that “continue to implicate the club in this type of practice”.
“Let one thing be clear,” Bartomeu continued. “To the question: Have we commissioned the monitoring of social networks? The answer is yes.
“To the question: Have we commissioned to discredit people or institutions through social networks? The answer is no and we will take action against all those who accuse us of that.”
The controversy increases the pressure on Bartomeu and the Barcelona board ahead of presidential elections due next year, and following a period of political turmoil at the club.
The board were clumsy in their sacking of coach Ernesto Valverde last month, when an approach to Xavi Hernandez was leaked while Valverde was still in post.
And two weeks ago, Messi engaged in a public spat with the club's technical secretary Eric Abidal, who claimed the players were the main cause of Valverde's removal.
The timing of this latest controversy is also a potential distraction ahead of a crucial week for the team.
Barcelona play Eibar at home in La Liga on Saturday before facing Napoli away in the Champions League and then Real Madrid in the league at the Santiago Bernabeu.