Leo Messi Magagement (LMM), whose president is the 26-year-old Argentine international's father, Jorge Messi, urged Spanish daily El Mundo to correct the story.
"Jorge Messi has never been connected to the case," LMM said in a statement. "He has not been investigated or called to testify, much less charged," it added.
"We hope that the newspaper El Mundo will correct the published story in line with the information released by the Interior Ministry," it said.
Spain's police and the Interior Ministry said a Colombian promoter was suspected of laundering drug money through concerts and sporting events in Spain, South America and the United States.
But they said there was no evidence of wrongdoing by Messi, his family or other players who featured in charity football matches organised by the Colombian promoter at the centre of the affair.
Besides putting on concerts in Spain, the Colombian firm, which has not been identified, staged charity football matches in South America and the United States featuring Messi, who is a four-time World Footballer of the Year, and other stars, police said.
Investigators had no evidence so far that the "Messi and Friends" charity football games were linked to money laundering, the authorities said.
The Barcelona forward's father had no link with the Colombian company, a police source said.
"He had nothing to do with this firm," the source said, playing down the report in El Mundo, which had described Messi senior as being "at the centre" of the affair.
Police said they took witness statements from football players to gather information about the company, but they were "ruling out for the moment their involvement in the crime being investigated".
El Mundo named the players as Barcelona's Messi, Dani Alves, Javier Mascherano and goalkeeper Jose Manuel Pinto. Barcelona coach Gerardo Martino said neither Lionel Messi nor his family were under any kind of investigation.
"Rumours cause damage when they are true but when they are not true they should not cause damage," Martino said. "There is nothing that should affect us," he said.
"It is notable that when the football is going fairly well, just at that moment rumours like this appear. We should treat them as such and stick to the reality, which is that there is no investigation" into anyone linked to the club.
Spanish police said they worked with Colombian security and the US Drug Enforcement Administration, arresting four people in the investigation, which began in April 2012.
Police said criminal charges had been laid against another eight people and four companies, and some 500,000 euros ($690,000) in assets had been blocked.
A Madrid examining magistrates' court, presided over by Judge Eduardo Lopez Palop, is supervising the case, which has been placed under seal, a judicial source said.
El Mundo deputy director Inaki Gil told AFP that the court, not the police, was in charge of the investigation. He stressed that El Mundo at no time suggested that Messi's father had been charged.
In an unrelated matter, Messi and his father appeared in court in September on charges of evading 4.16 million euros (USD 5 million) in taxes.
They denied wrongdoing, pointing the finger at a former agent. The famous duo had already repaid the tax authorities five million euros in August -- the 4.16 million euros claimed by the taxman plus interest.