The duty will be effective immediately, the ministry said.
The move comes amid steadily rising onion prices.
It is anticipated that onion prices will soar in September, especially ahead of the festive season.
Tomato prices also jumped in August despite government measures. However, the wholesale price dropped recently.
On Friday, the Centre instructed the National Cooperative Consumers Federation (NCCF) and the National Agricultural Cooperative Marketing Federation (NAFED) to sell tomatoes to retail consumers at a price of Rs 40 per kg starting from August 20.
Compared to previous months, potato and onion prices have risen.