Sources close to Shakira have previously denied that she evaded tax.
The charges, published Friday, allege that the Colombian pop star listed the Bahamas as her official residence for tax purposes during those years, even though she was living in Barcelona with her partner, Spanish soccer player Gerard Pique.
Spanish prosecutors charged Shakira with tax evasion.
The prosecutor alleges she avoided more than €14.5 million (RM68.3 million) in payments over a three-year period in which she lived in the north-eastern region of Catalonia, Europa Press reported.
Shakira started living with Pique in 2011, and in 2013, the couple had their first son, who was born in a Barcelona hospital.
They now want her to pay tax in Spain on the money she made in ventures around the world.
Prosecutors want Shakira to pay a bond of 19.4m euros (NZ$32m) - the amount they say she owes in tax, plus 33 per cent, in accordance with Spanish law.
They argue she was resident in Spain for most of the year, only travelling overseas for short periods.
A magistrate will now look into whether there is enough evidence to put the 41-year-old on trial.
The decision comes 11 months after Spanish judicial authorities announced an investigation into the singer's tax status.
Shakira was named in the "Paradise Papers" leaks that detailed the offshore tax arrangements of numerous high-profile individuals, including musical celebrities like Madonna and U2's Bono.
Officials are seeking the unpaid tax bill from all of her global income - not just the income generated in Spain.
In recent years, Spain has seen several high-profile court cases involving football stars accused of tax-dodging.
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