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.
Instead, they were "focused on preparing for the trial for the 2012-14 fiscal years, which will begin on Nov 20," they told Reuters in a statement.
The new charges hinge on the fact that in 2018, Shakira was living in Barcelona with football star Gerard Pique and was therefore required to tax all her international revenue there.
They argue that she instead diverted her money to "companies domiciled in countries with low taxation and high opacity".
Shakira faces trial over six separate alleged tax crimes in Barcelona this November - charges she has denied.
In that case, she has been accused of failing to pay €14.5m ($15.3m, £12.6m) in tax between 2012 and 2014, but has repeatedly denied any wrongdoing.
"I am confident that I have enough proof to support my case and that justice will prevail in my favour", she said in September, in an interview with the Spanish edition of Elle magazine.