An autonomous airspace separation system monitors flight separation for compliance with a separation standard. A reference formation airspace is established based on minimum longitudinal, lateral and vertical parameters. When penetration of the reference formation airspace is detected, a penetration airspace is established based on a deformation of the reference formation airspace caused by the penetrating aircraft. A centroid of the penetration airspace is determine and a target separation to the centroid is supplied to the aircraft to reestablish safe separation.