Bakayoko, who is on loan at AC Milan, was held up by police two weeks ago but the incident got wider attention this week after a video went viral on social media.
AC Milan confirmed that the reason for the search was due to a nearby shooting, and police have since insisted patting down Bakayoko was necessary given the seriousness of a dangerous situation taking place at the time.
In a statement released to Reuters, police said: "It should be noted that the search occurred in an operational context that justified the adoption of the highest security measures.”
"Also as a function of self-protection, and was carried out in a manner absolutely consistent with the type of alarm in progress.
"Once the person had been identified and established that he was not involved, the service was resumed without any kind of remark from the person concerned."
Bakayoko joined Milan on a two-year loan last summer, having also spent the 2018-19 campaign at the San Siro.
He made 14 appearances in Serie A last term as Milan won their first league title in 11 years.
Additional reporting by Reuters.