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Southern Archaeology director Dr Peter Petchey said four graves were found on Wednesday and two more yesterday.
The first two graves were found along the top of the 150-year-old cemetery, along the end of a row of graves, Dr Petchey said.
"Where we sort of expected we would find something."
Four of the graves were along the back fence of the cemetery, where there were no known graves.
"No-one even guessed there were graves there."
The first part of the investigation had been to remove topsoil which revealed the shape of the grave.
The more delicate work to reveal evidence of coffins and remains was beginning at two of the graves.
One coffin had very ornate coffin plates.
"We can’t read them, they are completely rusted away, but they are very ornate head, chest and feet plates on the coffin."
The coffins were covered in black fabric.
This was similar to the coffin style Dr Petchey had found during previous research at St John’s Anglican Cemetery in Milton, which dated from about the 1870s.
It was a plain wooden coffin made of rough sawn boards, and whole outside of the coffin was covered in a black fabric tacked in place.
"Then sometimes you had a decorative embossed metal strip tacked around the outside at the edge, and that would have been a silver cover."
Yesterday afternoon a surveyor also began marking out potential sites at the former Drybread settlement.
The settlement was established in about 1862 but was abandoned about 30 years later.
Work to uncover more about the site would begin next week with some exploratory digs, Dr Petchey said.