A former aide to retired West Publishing Co. executive Gerard Cafesjian has been indicted by a federal grand jury in Minneapolis on charges that he embezzled millions of dollars from his former employer over more than a decade and did not report the money on his income tax returns.

The indictment, which was handed up Monday and unsealed Wednesday, charges John Waters Jr., of Eden Prairie, with four counts of mail fraud, 16 counts of wire fraud, three counts of income tax evasion and three counts of filing false tax returns.

Waters, 56, started working for Cafesjian in sales and marketing at West Publishing in 1994. In a 2012 lawsuit, Waters said Cafesjian reaped about $300 million on the sale of West Publishing in 1996 when it was acquired by Thomson Corp., now Thomson Reuters. Waters left with Cafesjian to manage his considerable investments and philanthropic activities.

Cafesjian, who now divides his time between Roseville and Naples, Fla., is a patron of the arts and Armenian causes and the primary benefactor of the historic State Fair carousel that bears his name in St. Paul's Como Park.

Waters' suit alleged that Cafesjian stiffed him on $5 million in deferred compensation. Cafesjian denied that and countersued, alleging that Waters embezzled about $5 million from him.

The indictment, which largely mirrors Cafesjian's allegations, says Waters had signatory authority over a number of Cafesjian's accounts. It says that from 1999 into 2012, Waters transferred millions of dollars from those accounts to other accounts that he controlled, including one in the name of a deceased foreign exchange student. Waters dummied up Cafesjian's books and records and tried to keep others from reviewing them, the indictment says.

Prosecutors say that after Waters quit working for Cafesjian full time in 2009, he tried to keep his former boss from reporting the dispute to authorities and warned that harmful information would come out if he did.

In his lawsuit, Waters suggested that he believed he could expose embarrassing secrets about Cafesjian's private life, family and financial practices.

Cafesjian countered that he'd done nothing wrong and accused Waters of trying to "extort his way out of this by threatening scandalous revelations."

Cafesjian's attorney in the civil case is Andrew Luger, who has been recommended by U.S. Sens. Amy Klobuchar and Al Franken to replace B. Todd Jones, the outgoing U.S. attorney in Minnesota. Luger declined to comment on the indictment.

Dan Browning • 612-673-4493