The woman and her husband, both aged 44, appeared in Port Adelaide Magistrates Court on Friday, each charged with one aggravated count of committing an act likely to cause harm, which carries a maximum sentence of seven years in jail.
They are also charged with deception, accused of fraudulently raising $60,000 after putting their son in a wheelchair with bandages to imitate radiotherapy treatment.
The Adelaide couple had allegedly been requesting donations through an online fundraising page and the child's school.
The prosecutor told the court their children are "young, vulnerable and the safety of the alleged complainant is paramount".
Magistrate Alison Adair said a prosecution submission that the mother might impede the police investigation was a "valid concern".
She was open to considering another bail application early in the new year and ordered a home detention report for the mother, who will return to court on January 6.
The father will also remain in custody and Ms Adair adjourned his case until December 20.
"Having read the allegations, it appears this defendant is less involved than the other offender and in the circumstances, I'm prepared to consider home detention bail," she said.
Revealing the allegations earlier on Friday, Acting Assistant Commissioner John DeCandia said he "couldn't think of a more devious and cruel scheme that the parents have done to their own child".
"It's abhorrent that people would (allegedly) seek to profit for their own personal greed and selfishness from such an insidious condition such as cancer which impacts so many families in our community," he said.
The matter was reported to police on November 26 and the Western District Child and Family Investigation Section had been working with the Department of Child Protection, the child's school and Child Protection Services.
Mr DeCandia said daily risk assessments had been conducted to ensure the short-term safety of the boy and the couple's other child, a girl aged between six and 12.
"It will be alleged that the accused shaved their six-year-old child's head, eyebrows and placed them in a wheelchair with bandages to imitate stereotactic radiotherapy treatment," he said.
"Our investigation has confirmed the child is not seeking medical treatment. We believe this farce illness is causing significant and serious psychological harm to the child and their sibling.
"It's disgusting that these types of cases may ... have an impact on people who genuinely need that assistance. It would be terrible for people not to contribute to genuine causes because of a rare case such as this."
The children have been removed from the custody of the parents with a relative providing short-term care.
"There will be ongoing support needed for the child because initially thinking you've got cancer, and you're not well, would be quite devastating," Mr DeCandia said.
