The 54-year-old already settled a previous claim against him in 2014 which resulted in a penalty of €1.15 m, but tax authorities later found that some of the information presented in that settlement was incorrect, the prosecutors said.
The football world in Spain has been rocked by charges of tax evasion or corruption pressed against some of its top stars.
The case relates to the 29-year-old's image rights in 2012 and 2013, and he has agreed to repay £1.14million as well as a 60% fine.
Spanish prosecutors have filed a lawsuit against the player accusing him of defrauding tax authorities of 14.7 million euros (US$16.4 million) by hiding his image rights income between 2011 and 2014.
In an earlier report Marca said Ronaldo has told his teammates he was leaving and "there is no turning back".
This assumes, however, that Ronaldo is still a Madrid player, with a source confirming that he wants to leave Madrid and Spain as a result of accusations from the Spanish tax authorities and the media.
Ronaldo's future at Real Madrid looked guaranteed after lifting his third Champions League title with the club earlier this month, the Portugal global scoring twice in a 4-1 win over Juventus.
Ronaldo, who is in Russian Federation at the Confederations Cup playing for Portugal, has played in Spain for Real Madrid since 2009.
Manchester United manager Jose Mourinho has become the second big name to be fingered this summer after he was accused of two counts of fraud in 2011 and 2012 when he managed Real Madrid.
Mourinho's management team - Gestifute - and Real Madrid did not immediately respond to CNN's request for comment.
Under Perez, Real Madrid have won three Champions League titles in four seasons.
Ronaldo has become one of the biggest household names in professional soccer over the last decade and one of the most decorated players in the world, vying with Argentinian star Lionel Messi year after year for the top awards across both professional and worldwide football.
Mascherano was also convicted of tax fraud last year and was given a suspended one-year sentence.