The 18-month-old died in Waikato Hospital on July 24 following an incident at a Tirau address.
Detective Senior Sergeant Matt Cranshaw said today the woman's charges were in relation to offending against Comfort, but not in relation to her death.
The woman appeared in Rotorua District Court this morning.
Further charges are likely as the investigation continues.
Police would not comment further as the matter was now before the court.