The incident began at the Hospital for Sick Children last Wednesday, when the woman took in her 9-month-old son. Doctors determined the child was malnourished, as it weighed 11 pounds, close to a newborn's weight, The Globe and Mail reported Monday.
The 22-year-old woman reportedly abruptly left with the child, prompting police to issue an alert for the child's return.
Sunday, the mother and father returned to the hospital and kept police at bay for two hours before they were taken away to be booked on obstruction charges, the report said.
The couple belongs to a sect of Moorish-Americans who don't believe in institutionalized medicine and claim to hold dual Moroccan citizenship, the newspaper said.
The Toronto sect's leader, Grand Sheik Brother Kudjo Sut Tekh El, told the Globe the baby has eczema and severe food allergies, which has left him very thin. He said the religion has natural remedies for all ailments, including cancer.