Qari Yousuf Ahmadi said the Germans were shot to death. They had been kidnapped on Wednesday, along with five Afghan colleagues, in the southern province of Wardak while working on a dam project.
"The German and Afghan governments didn't meet our conditions, they didn't pull out their troops," Ahmadi told The Associated Press by telephone from an undisclosed location.
Ahmadi offered no proof for the claim of the killings; he said the Taliban would give further information about the two bodies later.
A spokesman for the German government and the nation's Foreign Ministry in Berlin could not immediately confirm the reports.
Militants on Thursday kidnapped at least 18 South Korean Christians riding on a bus in Ghazni, one province south of Wardak. Ahmadi said previously the Koreans would also be killed Saturday if South Korea didn't withdraw the 200 troops it has here, but he gave no information about their condition.
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Ahmadi warned the Afghan government and U.S. and NATO forces not to try to rescue the hostages, or they would be killed. The provincial police chief in Ghazni province said his forces were working "carefully" to not trigger any retaliatory killings.
"The enemy has threatened that there shouldn't be any kind of search operation for the Korean citizens," said Ali Shah Ahmadzai. "We have surrounded the area but are working very carefully. We don't want them to be killed."
Germany has 3,000 soldiers in NATO's International Security Assistance Force who are stationed in the mostly peaceful northern part of Afghanistan. South Korea has 200 soldiers in the U.S.-led coalition who largely work on humanitarian projects such as medical assistance and reconstruction work.
The troops run a hospital for Afghan civilians at the U.S. base at Bagram, and the facility has treated over 240,000 patients. The kidnapped civilians are not affiliated with the military.