German weekly Der Spiegel reported on Sunday that the country's BND secret service had spied on Turkey since 2009 and had listened in on at least one telephone conversation of US Secretary of State John Kerry.
Ambassador Eberhard Pohl was asked to provide a "formal and satisfactory explanation" over the reports and was told that if the claims were true, Germany should "immediately stop any spying activity targeting Turkey", the ministry said in a statement.
"Such practices would not be acceptable in an environment that requires mutual trust and respect between friends and allies," the ministry said.
"If the allegations have the slightest element of truth, it would create a serious situation that would need to be explained by Germany," the statement added.
However, a spokesman for the German Foreign Ministry said the ambassador had not been summoned but "invited" to the Turkish foreign ministry for "discussion".
"The discussion took place in a friendly atmosphere… It was to explain to the Turkish authorities what was published in the German media," Martin Schaefer told AFP.
Citing a confidential document, the magazine said the German government had chosen NATO ally Turkey as a top target for intelligence gathering in 2009.
Chairman of the Bundestag's Committee on Internal Affairs, Wolfgang Bosbach from Angela Merkel's ruling Christian Democrats, was quoted by the Kölner-Stadt Anzeiger as saying there were sure to be valid reasons for spying on Turkey, including monitoring the activities of certain left- and right-wing extremist groups, as well as the political and militant Kurdistan Workers' Party.
In Berlin, Green Party chief Katrin Göring-Eckhardt called on Chancellor Merkel to explain the allegations that Germany had spied on Turkey, as well as Secretary of State Kerry and his predecessor Hillary Clinton.
"We need to know how long the federal government has known about the BND's activities and how extensive this spying was," Göring-Eckhardt told the Passauer Neue Presse.
The vice-president of the parliamentary committee for the control of intelligence, André Hahn, from the socialist Left party, said: "It is high time that all the cards are laid out on the table."
Germany was outraged by revelations last year that US intelligence had allegedly eavesdropped on Merkel's telephone conversations.
Christian Democrat MP Hans-Peter Uhl, told the Bavarian state broadcaster that, in the case of Kerry and Clinton, the BND had accidentally recorded those calls, in contrast to the NSA purposefully recording Merkel's conversations.