The ruling makes her the first member of the country’s royal family to face charges in court since the royalty was restored in 1975.
In issuing the indictment, Judge Jose Castro went against a prosecutor’s 9 December recommendation that Cristina should be fined and only her husband, Olympic handball medallist turned businessman Inaki Urdangarin, be tried.
If convicted, she could face up to four years in prison.
Suspected abuse of company funds to cover the couple’s expenses at their Barcelona home, salsa dancing classes and stays at luxury hotels are among evidence Judge Castro has compiled about Aizoon, a real estate and consulting firm Cristina co-owned with her husband.
The case centres on allegations Mr Urdangarin used his Duke of Palma title to embezzle around €6 million in public contracts through the Noos Institute, a non-profit foundation he set up with a business partner that channelled money to other businesses, including Aizoon.
Lawyers for Cristina, King Felipe VI’s sister, have said she is innocent.
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Prosecutor Pedro Horrach recommended charges for Mr Urdangarin carrying a possible sentence of 19-and-a-half years in prison while saying Cristina should not be indicted but forced to pay €580,000 to cover the amount to which she could have profited due to her husband’s alleged illegal dealings.
Judge Castro had the option of accepting the recommendations or sending Cristina to be tried by a different judge.
The couple have 20 days to deposit the money or face having assets seized.
The judge set bail for 49-year-old Cristina at €2.7m and €15m for her husband. Others facing trial in the case include Jaume Matas, a former Spanish environment minister who has been convicted on other corruption charges, and several other former officials.
The investigation was pushed forward by Manos Limpias, or “Clean Hands”, a small civil servants’ union that acted as a private prosecutor in the case, a status allowed under Spanish law.
Last year, a Manos Limpias’ lawyer, Virginia López-Negrete, asked Judge Castro to name the princess as a suspect, on the basis of evidence that had surfaced after Mr Urdangarin refused to accept a plea bargain.
The evidence portrayed the princess as more actively involved in the work of her husband’s sports consultancy than she had previously admitted.
Cristina’s brother Felipe, 46, became king in June when his father Juan Carlos abdicated after a four-decade reign.
Felipe pledged to restore public trust in the monarchy and ordered a palace reshuffle, meaning that Cristina and her sister, Princess Elena, are no longer official members of the royal family, despite the troubled princess being sixth in line to the throne.
The case will probably go to trial at the end of 2015 in Palma de Mallorca, in Spain’s Balearic Islands, where most of the alleged offences occurred.
Cristina denied knowledge of her husband’s activities in February during an unprecedented appearance before Judge Castro.
She and her husband moved to Switzerland in 2013, where she works for the foundation of La Caixa bank, which finances programmes to help the needy and promote culture.
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