Pedro Rocha was named as president of the Spanish Football Federation on Friday by its electoral commission after a majority vote, despite a Spanish judicial corruption probe targeting Rocha and former RFEF president Luis Rubiales.
Spain's sports authority said on Thursday it will step in to oversee RFEF while the courts carry out a corruption and money laundering investigation into contracts that took the Spanish Super Cup to Saudi Arabia and federation links with Seville's La Cartuja Stadium, which hosts the Copa del Rey final and some international games, among other deals.
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Rocha and Rubiales have denied any wrongdoing.
Spain's Higher Sports Council said on Thursday it was taking the extraordinary measure for the coming months "in response to the crisis the institution is facing and in Spain's national interests."
The government has expressed concern for the reputational damage to the federation while Spain is set to co-host the 2030 men's World Cup with Portugal and Morocco. Spain is also hoping for success at this summer's men's European Championship and at the Paris Olympics.
The move by the government came two weeks after an investigating judge expanded a corruption probe to include federation president Pedro Rocha after the arrest of predecessor Luis Rubiales.
FIFA and UEFA, the institutions which govern world and European football, respectively, issued a joint statement saying they were closing watching the developments in Spain with "great concern."
They said they would seek "additional information" from Spain's Higher Sports Council to see how its oversight "may affect the (RFEF's) obligation to manage its affairs independently and without undue government interference."
Rocha took over as interim president after Rubiales stepped down in September, weeks after Rubiales became a national embarrassment for kissing a player without her consent during the Women's World Cup awards ceremony.
Information from The Associated Press was used in this report.