"German police authorities removed two passengers from the plane. We don't know the exact details, but all the passengers had to get out for a check of all the luggage, and they removed the suspects' luggage," a spokesman for KLM said.
The flight, KL1804, continued its journey to Amsterdam just over an hour later and has since landed in Amsterdam.
The arrests appear to be unrelated to a search for two suspected terrorists which the federal crime office had announced on Thursday.
The office had said they believed the two men, one German and one born in Lebanon, might be heading to Germany. They had previously thought they were in Afghanistan.
The men are linked to a foiled plot to attack United States targets in Germany in 2007.
Despite the search call and the incident in Cologne, Daniela-Alexandra Pietsch, a spokeswomen for the interior ministry, said the threat level in Germany had not changed.
Germany is still in the "crosshairs of terrorism'' but there are no indications of "concrete attack preparations,'' Pietsch said.