Webber, who led Michigan's "Fab Five" team to within a victory of the 1993 national title, was charged with obstruction of justice and making a false declaration before a grand jury.
Webber's father, Mayce Webber, also was indicted, FBI spokeswoman Dawn Clenney said.
The elder Webber did not immediately return a call seeking comment. The U.S. attorney's office and Michigan athletic director Bill Martin would not comment.
In May, former Michigan booster Ed Martin pleaded guilty to conspiracy to launder money.
Martin admitted he took gambling money, mixed it with earned income and money given to him from another person, then loaned it to at least four players while they were amateurs.
Martin said he paid $280,000 to Webber; $160,000 to Robert Traylor, now with the Charlotte Hornets; $105,000 to Maurice Taylor, now with the Houston Rockets; and $71,000 to Louis Bullock, who has been playing professionally in Europe.
Traylor and Bullock admitted receiving the loans in testimony to the grand jury, their attorney, Steve Fishman, has said.
Former Michigan guard Jalen Rose, now with the Chicago Bulls, also said in May that he took "pocket money" from Martin.
After Martin's indictment, Webber publicly denied taking significant amounts of money from him and said the government's charges were inaccurate.
Webber testified before the grand jury in August 2000.
"I answered all their questions, and I will help the prosecutors as much as I can," Webber told The Detroit News after testifying.
On May 28, Martin testified that he gave Webber cash and gifts and paid for other college expenses.
Webber, a 29-year-old four-time All-Star, was the first pick in the 1993 NBA draft and was rookie of the year with Golden State. He starred at Washington before being traded to the Kings.
Webber led Sacramento to the Western Conference finals, and the Kings were eliminated in Game 7 by the eventual NBA champion Los Angeles Lakers.