Qatari officials handed Germany's ambassador a letter highlighting Qatar's "complete rejection" of Interior Minister Nancy Faeser's comments, who had been due to visit Qatar on Monday.
Faeser, in an interview with the ARD network aired Thursday, said that Qatar's hosting of the World Cup next month was "very tricky" for Germany.
She added: "There are criteria that must be adhered to and it would be better that tournaments are not awarded to such states."
Faeser, in a statement released ahead of her visit with the head of the German football federation Bernd Neuendorf, said that rights would be raised in talks.
"No World Cup takes place in a vacuum. Human rights always apply everywhere - and now the whole world is paying special attention," Faeser said.
The demarche handed to Germany's ambassador stated that Fraser's statements were "unacceptable and provocative" and required a "clarification", Qatar's foreign ministry said.
This is the first time a foreign ambassador has been summoned by Qatar over such comments.
Qatar's emir Sheikh Tamim bin Hamad Al Thani said this week that his energy rich country had been confronted by an "unprecedented campaign" of "double standards" despite, he says, its labor and industrial safety reforms.
Rights groups have accused it of under-reporting deaths on construction sites over the past decade, and have campaigned for Qatar and football governing body FIFA to set up a compensation fund for workers.
Australia this week became the first World Cup team to release a statement on rights in the host country highlighting the "suffering" of workers.
Qatar responded by insisting that "protecting the health, safety, security, and dignity" of every worker was their "priority."
The spat comes at an awkward time for Germany, which has been negotiating for supplies of Qatari natural gas to make up for losses in Russian deliveries.
It is one of several European countries that have approached Qatar since Russia's invasion of Ukraine.