Prosecutors in the coastal state of Quintana Roo said Tahnee Shanks, 32, was last seen on Monday in Cancun.
There was no immediate information on how she became separated from her daughter.
But on Thursday, prosecutors also issued a missing persons alert for the girl's father, Jorge Luis Aguirre Astudillo, a Mexican citizen.
Aguirre Astudillo is also 32 and was also last heard from Monday.
According to a GoFundMe page set up in the name of the family of Tahnee Shanks, Aguirre Astudillo is believed to have dropped the child near a church in Cancun.
The girl was apparently taken into the care of child welfare authorities.
According to her Facebook profile, Shanks, from Conway Beach, Queensland, had been trying to get back to Australia.
Her plans were apparently delayed by the coronavirus pandemic.
Shanks wrote in May 2021: "I can't come back to Australia till mid 2022!!! My baby girl will be 2 1/2 years old and hasn't even met her grandad, uncles, great gran, cousins."
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