The Calgary-based chemical producer and oil and gas terminal operator (TSX:CUS) did not provide a reason for Kubera's departure.
Canexus has begun an international search for a new CEO.
In the meantime, Richard Ott, currently on Canexus' board of directors, will fill the role.
Kubera's exit comes less than two months after Canexus announced that its oil-by-rail terminal expansion project in Bruderheim, Alta., would be coming in at 40 per cent over the original estimate of $225 million.
In a Jan. 14 statement, Kubera said he was "disappointed" with the revised cost estimate, but noted Canexus had established a "state-of-the-art facility."