The newspaper, which has acquired Football Leaks documents, reported that the club gave the foundation "at least 12.7 million euros ($15.5 million) between 2010 and 2016".
The paper said that the payments from Barca represented 71.5 percent of the foundation's revenue between 2013 and 2016.
The foundation says on its website that it "was created in 2007 with the wish that all children should have the same opportunities to make their dreams come true, and to promote equality in education and health."
Those payments raised the suspicions of the authorities which, in January 2016, began to investigate whether the money had been "remunerative" and evaded corporate and income tax. In April 2016, tax investigators visited the Barcelona offices -- not for the first time in recent years.
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After the official scrutiny began, the club stopped making the deductions from their donations and started withholding 45 per cent for taxes suggesting, the newspaper said, that the payments "were considered part of the salary" of the Argentine star.
El Mundo said that, by law, 70 percent of a charity's revenue should be spent on the aims for which it was created but a report in another Spanish newspaper, ABC, found the foundation's accounts were full of gaps but included large sums spent on external consultants, rent and refurbishing its offices or transferred to its branch in Argentina.
That contract, which runs until 2021, will pay Messi more than 100 million euros a year including salary and image rights according to information published on Friday by the European Investigation Collaborations, which includes El Mundo.