"We should not underestimate the impact of large floods in Java, which supplies 60 percent of the nations food needs," he said here on Saturday.
Winarno estimated that 250,000 hectares of paddy fields nationwide were inundated during recent floods.
The floods which struck early this year were larger than those in previous years, he noted.
In the past, widespread flooding struck East Java. In 2014, several parts of Java, Sulawesi and Sumatra were flooded, Winarno said.
The floods had caused huge losses to farmers, he said.
"Much of the rice plantings have been flooded for more than three days now. If that is the case, the rice plants will not be strong and farmers will suffer losses," he said.
The government should assist these farmers by providing them with seeds and fertilizers, he said.
Coordinating Minister for Economic Affairs Hatta Rajasa stated on Wednesday that domestic food supplies are adequate, despite the floods having struck several parts of the country in the past few days.
"Reports from across the country reveal that our food staple stocks are adequate. Since there are no shortages, the prices of food commodities and food items have been relatively stable," he remarked, after a coordination meeting to discuss the food situation at the office of the state logistics agency (Bulog)s regional division for Jakarta and Banten.
Hatta noted that although food prices have risen, the increase has not been significant. Even the price of rice remains lower than that recorded in January 2013.
"The food items that saw a price hike include red chili, bird-eye chili, beef, and purebred chicken meat," he pointed out.
Reporting by Indriani
(EDITED BY INE)