Last week's floods - after a long dry spell of drought - in Andhra Pradesh and neighbouring Karnataka have killed at least 300 people and displaced more than a million people.
"Floods and drought have set back India's fight against poverty by years," said Jayakumar Christian, director of World Vision India, an aid agency working in the region.
Besides destroying standing crop, the floods have also contaminated grain stocks in millions of homes.
Though the government has not announced any plans yet to help residents deal with food shortages, Manmohan Singh, the Indian prime minister, has announced plans to visit the affected regions on Friday.
The floods came at a critical time when many farmers had sowed their winter crops and much of this has been washed away or damaged, Rao said.
Aid workers fear that the damage could set off a wave of migration to nearby towns and cities as desperate farm workers try to earn a living.