Some women prisoners - who are separated from their children - were being prevented from being able to express breast milk, Sisters Inside spokeswoman Debbie Kilroy said.
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Ms Kilroy said conditions for women prisoners were deteriorating with overcrowding.
The mother of the baby boy born 16 days ago in the Brisbane Women's Correctional Centre has been unable to provide breast milk for her child.
She was reportedly sharing a twin cell with two other prisoners and sleeping on a mattress on the floor.
Ms Kilroy said the baby was taken from the mother. Babies born in prison are normally allowed to stay with their mothers in special facilities.
"She is sleeping on a mattress on the floor because of the overcrowding in the prison," she said.
Authorities say the situation with the baby is more complex than described by Ms Kilroy.
Ms Kilroy said Sisters Inside had obtained a breast pump for the woman, but was told that extra paperwork had to be completed by the woman before the device could be provided.
"We acquired a breast pump today and took it out to the prison, but the prison refused to take the pump," she said.
"Because the mother has not put a form in to request it."
Ms Kilroy said Sisters Inside had to write to the woman and request her permission to provide her with a breast pump so she could approve it.
She said a different Aboriginal woman prisoner in a Townsville jail, who requested a breast pump after her baby was removed, was told by prison management to express milk into a urine sample jar.
"Because she was so distressed - the Aboriginal woman - they put her into isolation and they threw one of those urine sample jars at her," Ms Kilroy said.
"And told her to express into them.
"No, I am not kidding. Not kidding at all."
Authorities have disputed elements of Ms Kilroy's story, but said Queensland Health was now caring for the woman at the Brisbane Women's Correctional Centre.
Ms Kilroy questioned what happened to the "hundreds and hundreds of pages of of recommendations" from the review of the child support system, made by former chief magistrate Tim Carmody.
"Nothing has changed. It is actually getting worse for women inside," she said.
Queensland Corrective Services said the best interests of children born inside the prison were the highest priority for prison management.
"Mothers can apply to keep their baby with them in prison, with QCS – in association with Child Safety and other services - making the decision based on the best interests of the child and the mother," a spokesperson said.
"There is a mothers' unit at the state's women's prisons with accommodation specially designed for mothers with newborn babies.
"Due to privacy provisions, it is unlawful for QCS to discuss the personal circumstances of individual prisoners."
