According to Spanish radio station Cadena Ser Cataluna, the PR company I3 Ventures was contracted by Barca and 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 cites is one expressing anger towards Messi for his delay in signing a new contract and another questioning Pique's involvement in the Davis Cup.
But Barcelona released a statement on Monday that said the club "strongly denies any relationship and, furthermore, the contracting of services linked to social network accounts that have spread negative messages or disdain in relation to any person, entity or organisation that has or has had a relationship with the Club."
The statement said Barcelona hire "social media monitoring services" to keep track of posts written about the club but that I3 Ventures "has no relation to these accounts".
Barcelona also threatened legal action against any media organisations that "continue to involve the club in this type of practice".
The controversy increases the pressure on Bartomeu and the Barcelona board ahead of the presidential elections due next year, and following a period of political turmoil at the club.
The "Yes to the Future" campaign headed by rival presidential candidate Victor Font said in a statement the latest allegations were "extremely serious".
Bartomeu has admitted the club should have handled better the sacking of Ernesto Valverde last month, when an approach to Xavi was leaked while Valverde was still in post.
Then two weeks ago, Messi became embroiled in a public spat with the club's technical secretary Eric Abidal, who had claimed the players were the main cause of Valverde's removal.
Messi accused Abidal of "dirtying" the players, sparking fears the Argentinian could activate a clause in his contract that allows him to leave for free in the summer.
Bartomeu called a meeting with Messi and Abidal to stabilise the situation and another rapprochement may now be needed 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.
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