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The main aim of the Mission was to 'civilise' and Christianise the Aboriginal inhabitants of the area. Rations were provided to the Aboriginal residents on condition they attended church services and school.
At Ebenezer the residents attended three church services on Sunday, two for prayer and one for singing. The women and girls also attended Sunday school after each service.
Children were commonly separated from their parents and lived in dormitories attached to the mission manager's home or the schoolhouse. The managers undertook disciplining the children, even when it was directly against the wishes of the parents.
The buildings at the Ebenezer Mission increased to include a schoolhouse, girls' and boys' dormitories and cottages. In 1870 a girls' dormitory was constructed, but was used as a school from 1874. In 1873 a new building was erected which included a girls' dormitory and boys' dormitory. The dimensions of the dormitories were 18 feet long, by 20 feet wide, with 12 foot high ceilings. By 1874 there were eight beds in the boys' dormitory and 12 in the girls'. It was described as a substantial building with a corrugated iron roof and tongue and groove wooden floor boards and through ventilation.
As a result of the 1886 Act to Provide for the Protection and Management of the Aboriginal Natives of Victoria which forced half caste aborigines off missions, by 1892 the number of residents at Ebenezer Mission Station dropped to only 30 people.
The mission closed in 1904, and most of the land was handed back to the Victorian Lands Department and made available for selection.
In 1971 landowner Robert Bond gifted the freehold part of the land to the National Trust. It contains several nineteenth century Mission buildings including the kitchen, dormitory and toilet block and footings of the Mission House.
In 1980 the Trust acquired more land and in 2012 the Trust signed a Memorandum of Understanding with the Barangi Gadjin Land Council Aboriginal Corporation with a view to returning it to its traditional owners. This was accomplished in December 2013.
