The Griffith University research found the father-child relationship was greatly damaged by time behind bars and negatively affected children.
Susan Dennison, Professor of Criminology at Griffith University, carried out two studies.
One study looked at Indigenous and non-Indigenous fathers in south-east Queensland and one focused on Indigenous fathers in north Queensland.
Her report to government is titled "Vulnerable families: A study of Indigenous paternal imprisonment and its impact on Indigenous children, their caregivers and communities."
She said many of the prisoners in the two studies had fathers themselves who were absent when they were children.
"Many of them are part of stolen generations and so when we look at removing these men from their families and sending them to prison, we need to consider the impact that’s going to have on their children," she said.
Professor Dennison said 50 per cent of the fathers interviewed lived with their children before they were jailed, and a higher percentage had a relationship with their children prior to prison.
She said incarceration had damaged the father-child relationship with disastrous results across the generations and recommended the state government looked at improving access for children to fathers in prison.
Watch: The full report above.