In a written ruling the court on the island of Mallorca answered the latest appeals in a case that contributed to the abdication this year of Felipe's father, Juan Carlos.
The judges decided to "partially uphold the appeals... dismissing the proceedings with regard to money-laundering and maintaining the charges of cooperating in tax fraud" against Cristina, 49, they wrote in a ruling seen by AFP.
Judicial sources said the lesser tax fraud charges may yet be overturned by a separate investigating judge, who has the final say on whether Cristina goes on trial.
Investigating judge Jose Castro accused Cristina of knowingly benefiting from suspect business dealings by her husband, former Olympic handball player Inaki Urdangarin, the 46-year-old Duke of Palma.
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Urdangarin is himself accused of embezzlement. The judges today upheld a further charge of money-laundering against him.
Cristina's lawyers have insisted she is innocent and vowed to continue fighting the remaining charges.
"We are going to continue with the defence because we believe that there are not sufficient grounds to bring any kind of accusation," her lawyer Miquel Roca told reporters after today's ruling.
Urdangarin is accused along with a former business partner of creaming off six million euros (USD 8 million) in public funds from contracts awarded to Noos, a charitable foundation.
Cristina sat on the board of Noos and Urdangarin was its chairman.
Investigators suspect that a separate company jointly owned by the couple, Aizoon, served as a front for laundering the embezzled money.
Summoned by Castro in February, Cristina turned up smiling at the court and told the judge she had simply trusted her husband and had no knowledge of his business affairs.