TSA told WISN 12 News that the passenger was unaware of the screening protocol and did not tell security officers about her dog.
After an officer explained the proper process and confirmed she disclosed she was travelling with a pet to the airline, she proceeded to her gate.
TSA Great Lakes confirmed the incident was an accident on social media.
"A dog was accidentally sent through the X-ray @MSN_Airport this week," it tweeted.
"When travelling with any animal, notify your airline and know their rules.
"At the checkpoint, remove your pet from the bag and send all items, including the empty carrier, to be screened in the machine."
It then uploaded a video showing "the proper way" to travel with pets.
The incident comes mere weeks after a stowaway cat was found inside luggage at New York's John F. Kennedy International Airport.
If it hadn't been for the X-ray alerting officers to the stowaway, the cat would have been on a flight from New York to Florida.
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