The central Otjozundjopa region and the area surrounding the capital Windhoek were the most affected, with 24 positive cases reported in each area.
H1N1 influenza, also known as swine flu, is an acute viral respiratory infection in humans, often characterised by fever, headache, myalgia and other flu-like symptoms.
Namibia experienced a large-scale swine flu outbreak in 2009-10 when over 8,000 suspected cases were reported. During that outbreak, 102 people tested positive and one person died.
Children, elderly people and pregnant women are considered high-risk groups, the health ministry said, adding that a seasonal vaccination against H1N1 influenza was the best protection against the virus.