The recent classification of the koala to endangered across most of its range has emphasised the urgent need for enhanced disease surveillance. Little is known about the distribution and clinical significance of phascolarctid gammaherpesvirus 2 (PhaHV-2) outside the Australian states of Victoria and South Australia. PhaHV-2 may have significant impacts on koala wellbeing, justifying investigation into its distribution and impact. To better characterise virus distribution and factors associated with infection, we developed a novel quantitative polymerase chain reaction assay with a high sensitivity, specificity and throughput capacity, to facilitate rapid detection and quantification of PhaHV-2. We applied this assay to 157 predominantly clinically-derived, urogenital swab samples. Results indicated that the distribution of PhaHV-2 extends throughout the endangered New South Wales koala populations. Frequency of detection of PhaHV-2 was highest in South Australia (25%) and lowest in northern Qld (0%) and was more likely in older koalas than younger koalas. We corroborate previous findings of an association with presence of PhaHV-1 and find no evidence to support sex as a predictor for viral presence in clinically-derived samples. The capacity to rapidly detect mucosal shedding of PhaHV-2 will enable rapid isolation of affected individuals and aid further research into the pathophysiological impacts of this virus in koalas and the influence of co-infections.