The local structure of Mn impurities in ferromagnetic (Ga,Mn)N nanowires was investigated using extended x-ray absorption fine structure (EXAFS). By N2 plasma treatment, the nitrogen concentration increased and the ferromagnetic signal also increased. The EXAFS results showed that the Mn concentration occupying Ga sites increased and interstitially doped Mn atoms significantly decreased due to the plasma treatment. As a result, the N vacancies reduced and crystalline quality improved, resulting in the enhancement of ferromagnetic properties.