A 23-year-old Somali man and a 24-year-old German man born in Somalia were arrested without incident after officers entered the plane at 6:55 a.m. (0455 GMT), Katharina Breuer, a spokeswoman for North Rhine-Westphalia state police, told The Associated Press.
She said authorities did not think the men planned to hijack that specific flight but would not say whether they were armed.
Breuer said authorities had obtained a suicide note reportedly written by the men that stated they wanted to take part in "jihad" or holy war and die in a terrorist attack.
She would not disclose how authorities knew the men would be on board, but Germany's top-selling Bild newspaper, citing unidentified police sources, said the two had been under observation for months. Breuer did say the men lived in the area.
Police boarded the Fokker 50 jet when it was at its "point of departure" and grabbed the two suspects, KLM spokeswoman Elfrieke van Galen said, adding that the 46 remaining passengers aboard KLM Flight 1804 were then told to leave the plane.
"A 'baggage parade' took place to see if the two passengers who were taken by the police had bags with them," she said.
Van Galen said the plane took off after an hour's delay and landed at Schipol airport in the Netherlands without further incident. Cologne airport spokesman Alexander Weise said other flights were not affected.
Still, some people at the airport were rattled by the arrests.
"I saw a couple of policemen running out pretty quickly," said Antonietta Puzio, an airport cafe worker. "One always thinks something like this is so far away, and then something happens right by where you work."
The Dutch anti-terror chief warned earlier this month that the Netherlands remains one of the top targets for Islamic terrorist groups because of publicity surrounding a lawmaker's anti-Islam film.
The National Coordinator for Combating Terrorism said in a report the film "Fitna" by lawmaker Geert Wilders has made the Netherlands a "preferred target" for Islamic groups.
"Fitna" set Quranic texts against a background of violent images, which the agency said was "considered a major insult and provocation" by terrorist groups.
The country's terrorist threat has been rated as "substantial" since the film's launch in March.
Frank Wallenta, a spokesman for federal prosecutors in Germany, said the arrests in Cologne were not related to an earlier announcement that two men linked to terrorist suspects may be on their way back to Germany.
On Thursday, prosecutors said Eric Breininger, 21, and Houssain Al Malla, 23 could be headed to Germany after leaving a terrorist training camp in the border region between Afghanistan and Pakistan. The men are believed linked to the group involved in a foiled plot to attack American targets in Germany in 2007.
Despite the warning and the incident in Cologne, Interior Ministry spokeswoman Daniela-Alexandra Pietsch said the threat level in Germany had not changed.
Germany is still in the "crosshairs of terrorism" but there are no indications that specific attacks are planned, Pietsch said Friday.