An Air Force chaplain is being investigated over an affair he had with the wife of a corporal he was counselling over mental health issues.

Corporal Curtis Oliver, an armaments technician, had moved to RAAF Base Wagga Wagga in southern NSW early last year with his new bride Hailey Oliver, News Corp reports.

The couple, who grew up together in Geelong, Victoria, had reunited after both had suffered marriage breakdowns.

Mr Oliver was hit with depression and anxiety and turned to a chaplain attached to his squadron for help.

Counselling sessions then began with Chaplain Flight Lieutenant Michael Skilbeck.

Chaplain Skilbeck, a Baptist Pastor from Victoria, began to meet with Ms Oliver to discuss her husband's treatment — and at some point they began an affair.

She then left Mr Oliver in October 2013.

Chaplain Skilbeck, whose own marriage broke down, put Ms Olvier up in emergency accommodation at the RAAF base and paid her bond for a flat. They are currently living together as a couple.

Mr Oliver was finally sacked from the RAAF in May this year due to poor work performance but no mention was made of his mental wellbeing.

"He [Chaplain Skilbeck] reported back to my commanding officer and I wonder if he was getting me out of the picture for his own advantage," Mr Oliver was quoted as saying.