The southeastern state of Sao Paulo was the hardest-hit area, where 55 people were killed by the H1N1 flu, Xinhua cited the ministry as saying on Tuesday.
To stem the epidemic, Sao Paulo state started its flu vaccination campaign in late March, a month earlier than originally planned for the April 30-May 20 period.
Over the weekend, the state quickly ran out of vaccines as people rushed to hospitals to get inoculated.
“In previous years, you would buy the vaccine and have it administered the next day. Nowadays you buy it and you don’t know how much of or when you will receive the vaccine. Today it is quiet here because we don’t have any vaccines left,” said Katia Goncalves, director of a private clinic in Sao Paulo’s industrial suburb of Sao Caetano do Sul.
The ministry confirmed that it started distributing the doses to all the states on Friday and will deliver more.
Swine flu outbreak could not have come at a more inappropriate time, as Brazil prepares to host the Olympic Games in August, while struggling with its worst recession in decades and a sprawling corruption investigation into a state-owned oil company.
Nationwide outbreaks of Zika, dengue and chikungunya have also hit hard the Latin America’s largest state.