Ratna Dewi Umar, formerly the director for medical services, was found guilty on Monday of marking up the cost of medical equipment purchased in 2007 in preparation for a possible outbreak of the H5N1 bird flu virus.
The five-judge panel of the Corruption Court also ordered her to pay a fine of $45,000 or face an additional three months in prison. The equipment was used in a crisis response centre the ministry set up to deal with the threat from the H5N1 virus. More than 100 people died in Indonesia from the virus in 2007, making Indonesia the hardest-hit nation by the virus.
Ratna has denied any wrongdoing, telling the court she was carrying out orders from her boss, former Health Minister Siti Fadilah Supari.
Police named Supari as a suspect last year, but she has not been charged.
The Corruption Eradication Commission also questioned her last year, but Supari, who served as minister between 2004 and 2009, said she did not know the equipment purchases were suspicious.
The advocacy group Transparency International regularly lists Indonesia as among the most corrupt nations.