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Rural communities in Fiji, like many countries in the Pacific region, use on-site sanitation systems which have been linked to faecal-oral diseases like typhoid fever. This study aimed to explore the safety of existing sanitation infrastructure and to estimate the proportion of safely managed systems (SDG 6.2 targets). This study was conducted in 29 rural communities along five catchments across three islands of Fiji. Two data collection events occurred: household level survey and observations from 311 households (including soil sampling from a subset of 99 latrine back-ends) and community-wide sanitation safety planning (SSP) covering 1502 households. Self-reported back-end category results from the sanitation surveys were found to be very different from the technical back-end observation findings. Specifically, there was high self-reporting of septic systems back-ends by the households in the survey (240/311, 77%), however the observations revealed only 42/311 (14%) of households had access to a septic system (category 1). It was identified that the most common type of sanitation back-end was either category 2 tank type (19/311, 6%) or category 3 not visible tanks (161/311, 52%). Overall, 51–64% of the surveyed households over-reported septic systems and had a misconception that any tank type back-end (category 2 or 3) was a septic system. There was evidence of active faecal sludge leaching in the back-end surface leach zone soil, where Escherichia coliconcentrations were 6.5 times higher compared to unimpacted soil (p= 0.003). Safely managed sanitation was calculated for the first time and showed only 11% to 21% of surveyed households had access to a safe system. This study highlights the human health and environmental risks from unsafe sanitation and has implications for Fijian reporting against SDG 6.2 targets.