Health inspectors raided the cafe after reports of foul odors at the business, and an increasing number of kittens bred on the premises began to show signs of illness.
The business had reportedly been warned several times by the Tokyo Metropolitan Government's Bureau of Social Welfare and Public Health about poor hygiene, but did not comply.
"We issued repeated requests but there was no improvement," Yuriko Iwamoto, a spokeswoman from the Tokyo Metropolitan Government's Bureau of Social Welfare and Public Health told AFP.
"The property wasn't being cleaned properly and it was beginning to smell very bad," she added. "In line with animal welfare laws we were therefore forced to order them to cease business."
"There were more cats than cages," added Iwamoto. "The cages they did have were not properly controlled so they just multiplied."
The cafe licence has been revoked for 30 days.
As of 2015, there were reportedly 58 registered cat cafes across Tokyo.
