Critically important antimicrobials in medicine (CIA) should be used prudently to prevent the selection of serious antimicrobial resistant bacteria. However, the actual usage status of CIA in companion animal practices is unclear. Here, we conducted a questionnaire survey of the formulations, classes and target diseases of the major CIA used for dogs and cats at veterinary hospitals in Gifu Prefecture between April and June 2022. Classes of antimicrobials were used in 1,209 cases, with fluoroquinolones being used in 734 cases, third-generation cephalosporins in 467 cases and carbapenems in eight cases. Injectable formulations of fluoroquinolones and the third-generation cephalosporins were used more frequently in cats than in dogs. These agents tended to be used more frequently for skin/ear diseases regardless of species, but their use for other diseases varied by species. In conclusion, to promote their prudent use in companion animals, it is necessary to establish strategies based on animal species, formulations and common diseases.