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The awards were for most innovative education programme, most innovative public programme and the Arts Access Aotearoa Museums award.
The education award was for an exhibition titled ''Kia Rapua Science Playground'', and the most innovative public programme award was for ''Space Central''.
The ''iNDX'' exhibition, based on a project between the autistic community and advocates and the museum, won the Arts Access Aotearoa award.
Judge Judith Jones said the collaboration to create an exhibition of work by autistic artists ''really wowed us and had an impact far beyond the gallery space''.
The museum joined with the autistic community last year to create an exhibition of works by 28 autistic artists from Dunedin and around the country.
Tanea Paterson, an autistic woman who drove the project, said there tended to be a focus on the negative with autism, but the exhibition offered different viewpoints.
The Dunedin Public Art Gallery and Auckland Art Gallery Toi o Tamaki jointly won an award for art exhibition excellence, for the jointly-developed show ''Gordon Walters: New Vision''.