Aerodynamic winglets have been banned from Moto2 immediately, and will not be permitted in Moto3 beyond the end of this year.
Fairing winglets have become more prominent in MotoGP over the last 12 months, a trend started by Ducati.
LCR Honda rider Cal Crutchlow voiced his safety concerns that winglets could "slice" and injure riders in MotoGP during the Qatar Grand Prix weekend and riders are wary of the turbulence they create.
In the premier class, winglet development has been localised to the front fairing to help reduce wheelies, but the focus has been different in junior categories.
Winglets first appeared in Moto2 during the final pre-season test at Qatar earlier this month, but as downward-facing devices on the back of CarXpert Interwetten's Kalex machines.
These were designed to increase the turbulence felt by following riders, and following a decision by the governing body FIM, all winglets have been banned, effective immediately.
Front-fairing winglets have also emerged in Moto3 on the Aspar Mahindras to add downforce, and these will be allowed for the balance of the year, but not from 2017.
In both classes, "fairing designs used to deflect water displaced by the front wheel" without offering an aerodynamic gain are still allowed, the FIM confirmed.
Winglets are still permitted in MotoGP, but an off-season regulation change states that they must have rounded edges.