The woman, 20, who was not identified, has lodged an appeal which is due to be heard by the Family Court in Sydney on Friday.
The Sydney Morning Herald reported today that she had a finger and a foot tattooed in May without telling the tattoo artist she was breastfeeding.
It prompted the 11-month-old boy's father, who is separated from the mother, to take the toddler to live with him, claiming his former partner had mental health and drug issues.
The ruling came despite the woman recording negative results on hepatitis and HIV tests, the report said.
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The Australian Breastfeeding Association said it was worried that a dangerous precedent could be set.
"Tattooing is a regulated industry, so if you go to a tattoo parlour that is reputable then the chances (of contracting an infection) are very low," chief executive Rebecca Naylor told national radio.
"Tattooing in and of itself, as long as it's done in a reputable way and that the infection control procedures are followed, the risk is low and so no, we would absolutely encourage women who have had tattoos to breastfeed their babies for as long as they choose to."
She added that the ruling raised wider concerns.
"Does that mean that women who expose themselves to any sort of risks around the contraction of a blood-borne virus... shouldn't be allowed to breastfeed?" she asked.