"We are all calm," Barcelona president Sandro Rosell told a news conference in the northeastern city.
"His family have all of our support," he added.
"We do not have the slightest doubt of Messi's complete innocence in this matter."
The 25-year-old four time World Player of the Year and his father Jorge Horacio have flatly denied defrauding the Spanish tax authorities of more than four million euros.
Rosell said he had spoken to Messi's family in Argentina and they were calm in the face of the Spanish financial crimes prosecutor's allegations, which have shocked the sporting world.
He could not say, however, whether the club would provide legal support to the Argentina star.
"I do not know legally if we can speak in Messi's name, we have to discuss that with the legal services," Rosell said.
"The most important thing is to assure him that we are with him in everything."
Spanish financial crimes prosecutors filed papers with a court in Catalonia, northeastern Spain on Wednesday accusing Messi and his father of cheating on income related to the use of his image from 2006–2009.
The striker and his father aimed to deceive the state by ceding Messi's image rights to companies based in tax havens such as Belize and Uruguay so they would pay no tax in Spain, the prosecutor's complaint said.
"We are surprised about this news because we have never committed any infringement," Messi said in an English-language statement released on his Facebook account when the accusation surfaced.
The court has yet to decide whether to proceed with the case, but if it goes ahead it would be mark a major blow to Messi's near spotless reputation on and off the field.
The Argentine's achievements on the field have made him one of the most marketable sportsmen in the world and he was ranked 10th amongst Forbes' list of sports stars' incomes this month with an annual $21 million from endorsements alone.
The prosecutor's allegations, lodged with a court in Gava, near Barcelona, accused Messi and his father of defrauding the state of €1.06 million ($1.41 million) in his tax filing for 2007, €1.57 million in 2008, and €1.53 million in 2009.
Spain's press reacted with shock to the news.
"A symbol under suspicion," blared the front page of the country's biggest sports daily, Marca, saying in an editorial that he had cast doubt on his image as an exemplary sportsman.
"He has not been condemned, just accused, but the tax authority's account of a supposed fraud is hair-raising," the paper said.
The Barcelona-based daily Sport cautioned that the player had not been found guilty and should not be tried by the media.
"Messi does not deserve the injustice of parallel trials," the paper's director Joan Vehils said an opinion piece.
"Investigating him is fine but that he be condemned already without being given a chance to defend himself and without a trial is unacceptable."