The three Turks killed by an 18-year-old German-Iranian gunman were named as Sevda Dag, Can Leyla and Selcuk Kilic by the minister on NTV television.
“Three of our citizens were killed in the Munich shooting,” he said, adding that he had telephoned the families of the victims.
Greece said one of its citizens had also been killed, and three Kosovans were confirmed dead in the attack by their country's foreign ministry.
Sixteen others were injured, of whom three are in critical condition, Munich police said.
Most of the casualties were young people aged 15 to 21, Bavarian public television said.
The gunman is believed to have killed himself after the attack.
He began shooting at a McDonald's fast-food restaurant at the Olympia shopping mall near Munich's Olympic stadium shortly before 5 pm GMT on Friday.