A camshaft phaser control system for reducing rotor positional instability. A phaser system includes a target wheel mounted on the phaser rotor such that during camshaft rotation wheel teeth chop a signal to generate first and second interruption signals indicative of amplitude of rotor instability. An instability monitor is used to monitor the level of instability against predetermined acceptable levels, depending upon engine operating conditions (RPM, temperature). An excessive level of instability is established by engine calibration. When measured instability exceeds a predetermined threshold level for a predetermined period, an instability diagnostic becomes alarmed. A default strategy is used to correct the excessive instability by applying a bias to the phaser control duty cycle. The system continues to monitor the level of instability, and when instability falls below the threshold limit, normal phasing operation is resumed.