Christoph Ahlhaus told news agency AFP that the allegations, made in US magazine Vanity Fair in a profile of Erik Prince, founder of controversial private security firm Blackwater, should be subject to an "exhaustive enquiry."
"If there is evidence that US organs were active in Germany without the knowledge of their German partners, then the government should not continue with business as usual in its relations with the US," he said.
Vanity Fair said a CIA team was dispatched to Hamburg to "find, fix and finish" Mamoun Darkazanli, a Syrian-born German believed at the time to have known at least three of the hijackers who attacked the United States on September 11, 2001 who formed part of an Islamist cell in the city.
Darkazanli was detained by German authorities in 2004 after Spain's top terrorism judge, Baltasar Garzon, issued an arrest warrant against him, charging he acted as Osama Bin Laden's financier in Europe. But in 2006 German prosecutors dropped its investigation of the businessman, saying that although he had served as a contact for several al-Qaida members, he could not be considered as a member.
Vanity Fair cited an unnamed source as saying that the CIA team went in "dark," meaning they did not notify their own station, much less the German government, of their presence, following Darkazanli for weeks and worked through the logistics of how and where they would take him down. But officials in Washington chose not to pull the trigger, the magazine said.
On Monday a spokesman for Chancellor Angela Merkel said that he had no information on the allegations and that he was unable to comment. Prosecutors in Hamburg are reportedly currently determining whether there is sufficient information to begin an enquiry.
"I am speechless, quite frankly. This is a contract killing," Darkazanli said on ARD public television this week.