The virus was recently first detected in China, where there have been more than 40 cases and one death reported, reports Efe news.
The affected patient is a Chinese citizen in his 30s living in Japan's Kanagawa prefecture, south of Tokyo. Earlier this month he visited Wuhan, in China's Hubei province, where the outbreak originated, the Ministry said in a statement.
Tests conducted by the National Institute of Infectious Diseases were positive for the new type of coronavirus on Wednesday night.
The patient said he didn't visit Wuhan's fish and seafood market, where the outbreak is thought to have originated, but he may have been in contact with some of the affected patients.
The alert about the spread of the virus was raised after the first case outside China was reported in Thailand earlier this week. South Korea also reported a suspicious case last week.
The Japanese Ministry of Health confirmed in the statement that they will conduct preventive epidemiological studies and collaborate with relevant organizations, such as the WHO, to assess the risks.
Japan has urged its residents to practice good hygiene and go to a medical centre as soon as possible if suspicious symptoms develop.
Coronaviruses usually cause common cold-type symptoms and are spread through sneezing, coughing or direct contact.
However, some types lead to more serious, sometimes deadly respiratory diseases, such as severe acute respiratory syndrome (SARS) or Middle East respiratory syndrome (MERS).
( With inputs from IANS )