The Chicago-based airline said a flight attendant who ordered the passenger to put her pet carrier in the overhead bin aboard a Houston-to-New York flight Monday didn't know there was a dog inside.
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"To prevent this from happening again, by April we will issue bright colored bag tags to customers traveling with in-cabin pets," United said in a statement.
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The family that owned the dog and other passengers contradicted the airline's account, saying the dog's barks were audible from inside the bin.
Eleven-year-old Sophia Ceballos told NBC News that her mother told the flight attendant "'It's a dog, it's a dog,' and (the flight attendant) said we have to put it up there," in the bin.
Other passengers backed up the family's account on Twitter and Facebook.
Late Wednesday, the Harris County, Texas, district attorney's office said its animal cruelty division is working with the county's animal cruelty task force on a criminal investigation about what happened on the plane.
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A statement from prosecutors said they won't decide if criminal charges are warranted until the investigation is completed.
The Associated Press sent an email seeing comment Thursday on the criminal investigation to an airline spokesman.
Last year, 18 animals, mostly dogs, died while being transported on United - three-fourths of all animal deaths on U.S. carriers, according to the Department of Transportation. Those figures represent animals that die in cargo holds.
It is rare that an animal dies on a plane. Even on United, there was only one death for roughly every 4,500 animals transported last year.
United, which promotes its pet-shipping program called PetSafe, carries more animals than any other airline, but its animal-death rate is also the highest in the industry. Alaska Airlines, which carries only 17 percent fewer animals, had just two deaths last year.