The incident happened at around 5:30pm when the man's car collided with a jeep on the Bantry to Crookestown Rd east of Togher Village.
The man, who is in his 30s, was airlifted to Cork University Hospital where he is described as being in a critical condition.
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Another man, the driver of the jeep, was also taken to CUH where he remains in a serious condition.
Gardai are appealing for any witnesses to contact them at Clonakilty Garda station.
