As his career progressed in the NBA, Mathis achieved greater influence among officials by serving on the executive committee of the NBA referees union from 1990 to 1997. During the period, he was involved in the negotiation of a new contract for referees, who went on strike to start the 1995–96 NBA season.
Airline ticket income investigation
During the late 1990s, many NBA referees became the target of an Internal Revenue Service investigation of cash received as a result of the sale of first-class airline tickets for less expensive ones. The IRS claimed this was additional income that went unreported. In 1997, Mathis was indicted for falsifying income on tax returns and immediately resigned from the NBA. The following year, he pleaded guilty to tax evasion for understating income by $69,000 from 1989 through 1992. Mathis admitted to trading in first-class airline tickets provided by the NBA for cheaper, coach-class tickets and pocketing the difference and using several means to conceal income generated from downgrading seats, including obtaining bogus airline receipts and invoices from a travel agent in Denver, Colorado. A few months after pleading guilty, Mathis was sentenced to 120 days of home confinement, three years of probation, 200 hours of community service, and a $2,000 fine.
Return to the NBA
After nearly a two-year hiatus from the NBA, Commissioner David Stern reinstated Mathis and several other referees in January 1999 who were found guilty during the investigation. During his second stint in the NBA, Mathis officiated for two and a half seasons before retiring following a game played on December 16, 2001 in Seattle, Washington. He closed out his career as Seattle SuperSonics team officials at KeyArena shined a spotlight on him during a timeout and spectators gave him a standing ovation.
Post-NBA officiating career
Mathis returned to the Seattle area following retirement to serve as a team consultant for the SuperSonics on rules violations. Mathis has been an outspoken critic of the NBA's evaluation system of referees and league supervisors following allegations that former NBA referee Tim Donaghy was betting on league games. Mathis felt that only friends of league officials are hired to fill openings and the current supervisors are not qualified to do their jobs since he claims that "they were once referees, and they were fired. These are guys who should be teaching and training refs, but they have no business in those positions."
Barkley Vendetta
On May 10, 2009, Charles Barkley stated on TNT's Pregame show that Mike Mathis is the only NBA referee that did not want to get all of the calls right, all of the time. He also later stated that Mathis was the worst official of all time. Barkley reiterated this point during halftime of the Marquette University vs. Syracuse Orangemen NCAA Tournament basketball game on March 20, 2011, and during halftime of Game 3 of the Los Angeles Clippers vs. Golden State Warriors2014 NBA Playoffs when he said that most professional and college referees were good at their jobs, with the sole exception of Mike Mathis. During the Golden State Warriors vs. Los Angeles Clippers playoff broadcast on April 24, 2014, Barkley said, "Most refs are good guys, except Mike Mathis, he's not a good guy." On the February 11, 2016 edition of Inside the NBA, Chuck said he respected all referees except Mathis. Barkley reiterated his distaste for Mathis on April 30, 2019 during the TNT pre-game show during the Golden State Warriors vs. Houston Rockets playoff broadcast.