The blockade and lengthy searches of each and every arriving ship created a long line to get into the Iziz Starport, creating a tense atmosphere and ruining merchant shipping schedules. The Onderonian navy briefly fought a fleet of commercial ships in waiting to land on their planet, after it attempted to destroy the Ebon Hawk, a Jedi vessel, inadvertently causing the nervous freighter fleet into thinking it was coming under fire. The merchant ships returned fire and the Onderonian navy lost a number of single-seat fighters and possible damage to some of its capital ships before the fighting was stopped.
The navy was most likely divided in its loyalties just as the ground forces of Onderon were during the Onderon Civil War, but what happened in the Onderonian navy during the war is unknown.