Rachel Koechner, 28, is awaiting formal charges after she made false allegations she and her daughter Zoee, 4, had been abducted, Chariton County Sheriff Chris Hughes said.
The two were reported missing on Thursday by Koechner's mother, KRCG-TV, Jefferson City, Mo., said.
Police added Koechner called authorities from a local motel, but was not there when they arrived Monday morning.
Koechner's ex-husband, Devon Sandner, was also taken into custody for outstanding warrants on forgery charges, the television station said.
Hughes said the child was unharmed, and in state protective custody.
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