The operation followed intense criticism of the police for failing to protect hundreds of women from being sexually molested, mostly by North African men, a year ago.
In a desperate attempt to stop a repeat of the horrid scenes, Cologne officers screened individuals on the street and stopped around 650 people in total.
As police shared their efforts with the public on social media, criticisms poured in as they were accused of being racist for stopping mostly North African and Arab men.
Despite the harsh criticisms of the police, a YouGov poll has revealed two thirds of Germans supported the decision to racially profile the immigrants.
Following the online row Cologne Police chief Juergen Mathies insisted his force had acted appropriately.
He said: “I reject this negative criticism. The clear aim was to prevent similar events to the previous year.
Approximately 100 people were arrested in Cologne night to January 1 however it has not been made clear whether the 650 detainees were among that figure.
Authorities said more than 150 crimes had been reported during the celebrations, including almost a dozen assaults or insults of a sexual nature.
It comes as the Berlin branch of the far-right party Alternative for Germany (AfD) has advocated the profiling of “certain groups of offenders” based on their “cultural backgrounds”.
Mr Pazderski said: “We know of course that there are certain groups of offenders from certain regions who commit certain offences.
“And when I conclude in a statistic that certain ethnic groups increasingly commit certain offences, I will have to look into it in detail, find the cause of it and take action.
“It could, for example be connected with the cultural background.”