A 23-year-old Somali man and a 24-year-old German born in Somalia were arrested before the KLM flight left the airport, North Rhine-Westphalia state police said.
A KLM spokeswoman said on NOS news in the Netherlands that police boarded the plane when it was at its "point of departure" and grabbed the two suspects.
Everyone was then forced to leave the plane, and there was a "baggage parade" to see whose bags belonged to whom, she said.
No further details were immediately available.
Germany's top-selling Bild newspaper, citing police sources, said the two had been under observation for months and a suicide note was found in their apartment saying that they wanted to die for the "jihad" or "holy war."
The arrests came one day after officials said they were searching for two men linked to a group of terrorist suspects whose alleged plot to blow up American targets in Germany was foiled in 2007.
Eric Breininger, 21, and Houssain Al Malla, 23, are believed have been training at a terrorist camp in the border region between Afghanistan and Pakistan, federal prosecutors' spokesman Frank Wallenta said.
It was not immediately clear whether there was a link between Friday's arrest and the search for Breininger and Al Malla.
Authorities issued an arrest warrant for the pair in April, but did not release their names at that time as they sought to find them through cooperation with other agencies internationally. They decided to go public with the information on Thursday amid suspicions the men may have been on their way back to Germany.
Both men are suspected of membership in a foreign terrorist organization and have been under investigation for "a fairly long time," Wallenta said.
Breininger and Al Malla are thought to be linked to the al Qaeda-affiliated group that is alleged to have plotted attacks within Germany that were intended to kill as many Americans as possible, Wallenta said.
Still, there is no "immediate suspicion" that they were involved in the plot themselves, he said. He noted that unlike the three suspects charged in that case, Breininger and Al Malla are being sought as members of a foreign, rather than domestic terrorist group.
No attacks were carried out.
The principals in the main group, Adem Yilmaz, 29, a Turk living in Germany; and two German converts to Islam, Fritz Martin Gelowicz, 29, and Daniel Martin Schneider, 22, were charged in early September with membership in domestic terrorist organization as well as membership in a foreign terrorist organization in the plot allegedly led by Gelowicz.
Another man, Attila Selek, a 23-year-old German national, was arrested in November 2007 in Turkey, and Germany is seeking his extradition. A fifth suspect, identified only as Dana B., remains under investigation, Wallenta said.
The three suspects charged this month operated as a German cell of the radical Islamic Jihad Union - a group the U.S. State Department says was responsible for coordinated bombings outside the U.S. and Israeli embassies in July 2004 in Uzbekistan - according to prosecutors.
The group is alleged to have scouted possible targets, including the U.S. military's base in Hanau, Germany, and stockpiled hundreds of pounds of highly concentrated hydrogen peroxide at a German cottage. The chemicals were enough to build bombs equal to at least 900 pounds of dynamite, prosecutors said.
Authorities say the group was never close to reaching its goals.
German authorities - acting partially on intelligence from the U.S. - covertly swapped out all of the hydrogen peroxide with a diluted solution that could not have been used to make bombs.
Last week, two other men - identified only as Omid S., 27, and Hueseyin O. - were arrested in the Frankfurt area on suspicion of involvement with the group. There was no "immediate suspicion" they were directly part of the plot, Wallenta said.