Bioarchaeologist Associate Prof Sian Halcrow, of the anatomy department, led an international research team focusing on the tiny mummified body, known as the Atacama Mummy.
Prof Halcrow said the Otago evaluation of earlier skeletal and genomic research at Stanford University raised several "concerning" issues over ethics, and the need for multidisciplinary approaches to such DNA research, and for more open scientific debate, she said.
The Otago research was published in the International Journal of Paleopathology this week.
The Stanford work was published in Genome Research earlier this year.
In April, Lisa Matisoo-Smith, a professor of biological anthropology, also of the Otago department, spoke out in an address to a science communication conference in Dunedin.
Prof Matisoo-Smith discussed some overseas-based genetic researchers, who did not always engage fully with local communities and use the careful, multi-disciplinary approaches needed to avoid potential DNA analysis problems.
Earlier problems had included questionable DNA analysis of skulls, which may have been mislabelled in a Latin American museum, and issues with other skulls found in Pacific graves.
Prof Halcrow agreed with Prof Matisoo-Smith's concerns, and said the latest Otago-led research, involving a tiny mummy, nicknamed Ata, highlighted related issues.
The mummy was discovered more than a decade ago in an abandoned town in the Atacama Desert, in Chile.
The Stanford researchers concluded genetic abnormalities could explain perceived abnormal characteristics of the skeleton, which was only 15cm long.
But Prof Halcrow and fellow university researchers in the United States, Sweden and Chile, raised concerns about the earlier analysis.
The earlier "scientifically flawed" study highlighted the need for slow research, with input from other key specialists, including in bone development and archaeology, she said.