The 23-year-old faced the District Court in South Australia charged with criminal neglect and endangering the life of the child, who survived the ordeal.
The woman, whose name cannot be published, denied endangering the youngster's life and pleaded guilty to the lesser charge of neglect.
But prosecutors rejected her plea and she will be tried on the higher charge.
A neglect charge was dropped against the boy's 27-year-old father after he pleaded guilty last month to endangering his son's life.
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A police witness statement said the boy was "unable to stand" when he was found and "appeared to struggle to speak and shook as he did", the Advertiser newspaper reported.
The father said in a police interview that his son was allegedly locked up because he was naughty.
"Nothing bad," he told police, according to the Advertiser, adding that they were "not negligent parents or anything".
The father said the son was fed with food sachets, biscuits and long-life custard, but was given no water.
"He hasn't learnt to drink out of a sippy cup yet," the father said in response to police questions. "We tried teaching him, he just won't snap to it.