Prosecutors in Spain allege the singer defrauded the state of €6.7m ($7.1m, £5.8m) in 2018.
They say this happened when she failed to declare millions in advance payments for her El Dorado World Tour, among other payments.
Spanish prosecutors opened the second investigation in July 2023, but released the details on Tuesday.
Spanish network RTVE says the 46-year-old singer is aware of the new charges, but news agency Reuters reports that Shakira's legal team in Miami - where she now lives - has not yet been told about them.
