An unidentified person who came back to France from a trip to the United Arab Emirates was diagnosed with the deadly novel coronavirus, the ministry said.
"This is the first and only confirmed case in France to date," it added.
The patient is currently in intensive care in hospital and has been placed in isolation.
The virus, known in medical jargon as nCoV-EMC, was first detected in September 2012 and since then more than 30 cases have been reported in different countries, with 18 deaths.
While it has been deadliest in Saudi Arabia, where 11 people have been killed by the virus, other cases have been reported in Jordan, Germany, Britain and now France.
It is a cousin of Severe Acute Respiratory Syndrome (SARS), which triggered a scare 10 years ago when it erupted in east Asia, leaping to humans from animal hosts and eventually killing some 800 people.
Like SARS, the new virus appears to cause an infection deep in the lungs, but it also differs from SARS in that it also causes rapid kidney failure.
The World Health Organisation does not so far have enough information to determine how the virus is transmitted or from where it originates, but it has called for international vigilance.