The man died in the town of Ostercappeln, north-west Germany on June 6 from complications stemming from the virus, the ministry said in a statement.
It is the first German death from the MERS virus, which emerged in the Middle East in 2012 and is from the same family as the SARS virus. It can cause coughing, fever and pneumonia.
The man is believed to have been infected with the virus while visiting an animal market on the Arabian Peninsula in February, the ministry said.
It said there were no indications he had infected others, having tested 200 people and found them all negative for the virus.
The virus has infected over 150 people in the Republic of Korea and killed 19 of them since it was first diagnosed on May 20 in a businessman who had returned from a trip to the Middle East.