In a statement, the network and production company Shine America said they and trainer Michaels have decided to part ways, and she won't be back on "Biggest Loser" this fall.
This is the third time that Michaels, known for her tough, drill-sergeant approach to working with contestants as they shed pounds, has left the series.
Asked if she might return again, a production company spokesman said the focus was on the upcoming season, No. 16.
There was no immediate response Wednesday from Michaels' representative to an email request.
Michaels' replacement on "The Biggest Loser" was not announced.
The well-muscled Michaels has described herself as a formerly overweight, unhappy youngster who found a path to fitness through martial arts, eventually becoming a trainer, physical therapy aide and then sports-medicine professional.
In 2012, Michaels returned for the show's 14th edition after taking a break to pursue adoption of a daughter. She and her partner also have a son.
"The Biggest Loser" provoked a debate in February when contestant Rachel Frederickson won after a huge weight drop that took her from 260 to 105 pounds. Criticism arose on social media about whether she'd lost too much, while experts questioned the focus on body size rather than overall health.
People Magazine reported that In April, a source said Michaels, 40, was "deeply concerned about the direction the show has been taking" after winner Rachel Frederickson's appearance in the finale sparked backlash over her thin frame.
The series is scheduled to return to NBC in September.
Michaels said she feels that it's inhumane to make the animals work in Central Park and on Manhattan's streets.
Mayor Bill de Blasio wants to ban the carriages and replace them with vintage-looking electric cars. But he may not have enough votes in the City Council to pass a law. Other celebrities, including Alec Baldwin, Pink and Lea Michele also support the ban.