Investigators have been told the man was investigating a barking dog at a property on Silesia Court Merrivale about 3.50am Sunday.
The 28-year-old Warrnambool man heard a loud bang and then realised he had been shot in the leg.
The man walked to the Warrnambool hospital where police were alerted of the incident.
S.E.S and police have been searching an area in a reserve opposite the Merrivale football oval Sunday morning for evidence.
The investigation is ongoing and anyone with information is urged to contact Crime Stoppers on 1800 333 000.