In Australia, under the National Assessment Plan, educational accountability testing in literacy and numeracy (NAPLAN) is undertaken with all students in Years 3, 5, 7 and 9 to monitor student achievement and inform policy. However, the extent to which these data have been analysed to report student progress is limited. This article reports a study analysing Year-3 and Year-5 NAPLAN reading and numeracy data, school and student information for a single student cohort from Queensland, Australia, to examine student achievement and progress. The analyses use longitudinal multilevel modelling, incorporating an enhanced approach for missing data imputation, given that such data frequently involve large amounts of missing data and failure to account properly for such missing data may bias interpretations of analyses. Further, statistical adjustments to deal with the impact of measurement error, an aspect not previously addressed in such analyses of data, are undertaken. A special focus of analyses is achievement of Australian Indigenous and non-Indigenous students. International and national data demonstrate a considerable achievement gap between these students. "Closing the gap" is a core Australian education equity policy, with NAPLAN data used as a primary indicator of policy impact. Overall, analyses indicate greater understanding of student progress for all students is available from Australian data if appropriate analyses are undertaken. However, analyses also demonstrate not only that the gap between Australian Indigenous and non-Indigenous student progress increases as they move through school but also diversity of achievement within the Indigenous student cohort. Implications for policy are considered.