The mosque officials told Anadolu Agency that the mosque complex, which houses the headquarters of the Turkish-Muslim umbrella group DITIB, was evacuated in the afternoon after receiving a bomb threat via telephone.
Police cordoned off the mosque complex and began a thorough search of the buildings.
It was the second time in four months Cologne Central Mosque has received a bomb threat.
In June, an email containing a similar threat had forced the evacuation of visitors and staff from the mosque complex. After a thorough search, police determined the threat was a hoax.
Germany has witnessed growing Islamophobia in recent years triggered by far-right propaganda.
More than 100 mosques and religious institutions were attacked by far-right extremists in 2018.
Police recorded 813 hate crimes against Muslims last year, including insults, threatening letters and physical assaults. At least 54 Muslims were injured in the attacks.
Germany, a country of over 81 million people, has the second-largest Muslim population in Western Europe after France. Among the country’s nearly 4.7 million Muslims, 3 million are of Turkish origin.