Bowles said Wilkerson will not make the trip to New Orleans, calling it a "coach's decision."
"I'm worried about the guys I'm coaching," Bowles told reporters. "I'm not worried about Mo."
According to multiple reports, the 28-year-old Wilkerson arrived late to Friday morning's team meeting and tardiness continues to be an issue for the former Pro Bowler.
Wilkerson was benched for the first quarter of the Dec. 3 game against the Kansas City Chiefs because he showed up late for a meeting on the eve of the contest. He also was fined by the team.
It marked the third straight year that Wilkerson had been benched for a quarter for disciplinary reasons, according to ESPN.
Wilkerson, who signed a five-year, $86 million contract in July 2016, has only eight sacks in 28 games since the new deal. The Jets likely will release him before March due to lack of performance and because his $16.75 million salary becomes fully guaranteed if he is on the roster for the third day of the 2018 league year.
Wilkerson, the Jets' first-round pick in 2011, posted a career-high 12 sacks in 2015. The Jets used the franchise tag on Wilkerson for 2016, but the sides worked out a long-term agreement minutes before the July 15 deadline last season.