The Qatari patient suffers from asthma and has been in contact with another patient infected with MERS.
He is "in a critical condition and is under intensive care," the Supreme Health Council said in a statement yesterday.
On August 20, the authorities announced the first infection in the Gulf state of a 59-year-old Qatari.
Another Qatari national with the infection died in a London hospital on June 28.
The virus has killed 47 people worldwide since September, 41 of them in Saudi Arabia which neighbours Qatar.
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Like SARS, it is thought to have jumped from animals to humans, and shares the former's flu-like symptoms -- but differs by causing kidney failure.
Researchers have pointed to the Arabian camel, or dromedary, as a possible host of the virus.
Scientists studying the new virus have found older patients, men and people with underlying medical conditions are those particularly at risk.