Despite the long-standing cultural, environmental, and spiritual relationship between First Nations peoples and dugongs, Indigenous knowledge systems remain largely marginalised within Western scientific research. Here, we examined the extent colonial legacies influence contemporary dugong (Dugong dugon) research in South-East Queensland (SEQ), with particular focus on the representation of Indigenous Ecological Knowledge (IEK). A systematic review and qualitative content analysis were conducted on 42 peer-reviewed scientific publications on dugongs in SEQ over the last 25 years, spanning various topics, including biology, conservation, and archaeology. Results revealed minimal Indigenous inclusion. Only one publication (2.5%) incorporated Indigenous language, while the majority relied exclusively on Western scientific terminology. Indigenous co-authorship was absent, and formal acknowledgement of Traditional Owners occurred in only two studies (5%). Although 45% of publications referenced Indigenous peoples, only five met more than one inclusion indicator, indicating largely superficial engagement. In contrast, Indigenous-authored and Indigenous-led literature demonstrated holistic understanding of dugong ecology that integrate ecological, cultural, and spiritual dimensions, which are largely absent from Western scientific discourse. Meaningful decolonisation of dugong research requires restructuring marine science to centre Indigenous frameworks, authority and ontologies, enabling genuinely collaborative and decolonised research practice.