Federal prosecutors say Hill earned more than $1.6 million in 2005, 2006 and 2007 - the three years she failed to file returns.
Prosecutors say Hills' primary source of income is royalties from the recording and film industries. She also owns and operates four corporations: Creations Music Inc., Boogie Tours Inc., L.H. Productions 2001 Inc. and Studio 22 Inc., according to court papers.
Hill, who lives in New Jersey, is scheduled to appear before a federal magistrate on June 29. She could face a maximum of one year in prison and a $100,000 fine on each charge.
The 37-year-old got her start with The Fugees and began her solo career in 1998 with the critically acclaimed album "The Miseducation of Lauryn Hill." The album, which mixed rap and soul, sold eight million copies.
She then largely disappeared from public view to raise her six children, five of whom she had with Rohan Marley, the son of famed reggae singer Bob Marley.
The Associated Press contributed to this report.