Police are now searching for the baby's father, Randy Hughes. Investigators said he disappeared a few days after the reported abuse.
Police said Hughes was watching the baby and other older children at their home while the baby's mother was at work.
According to the criminal complaint, when his wife confronted him about the bruises, he said he was "going to jail." But when doctors questioned him, he said the baby fell from the bed and that he saw a 4-year-old "run" from the room right afterward.
Doctors said the baby has nine broken ribs, two broken legs, lacerated liver, internal bleeding and bruising about her left eye and right ear.
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The emergency room doctor told police she would have been in "substantial pain for multiple days and could have had a life-threatening hemorrhage from the liver laceration" and that it was not from a fall or another child.
Hughes faces arrest on felony aggravated assault and child endangerment charges.
The baby had a follow-up appointment at Children's Hospital on Monday, and doctors said she is healing very well.
The mother passed a polygraph test, and police said they believe she had nothing to do with the abuse.