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The storms have also affected wheat in Madhya Pradesh and Uttar Pradesh, states which produce high quality wheat.
The damage to rapeseed could mean India imports more rapeseed oil, which is made from rapeseed. That could push prices higher as India is the world's biggest buyer of edible oils. The April rapeseed contract rose 6.7% over the last ten days, while rapeseed oil firmed 0.7%.
India is also the world's largest buyer and consumer of pulses and damage to the crop would increase buying.
Last month, the government forecast record production of wheat, chickpea and rapeseed. The Solvent Extractors' Association (SEA) also recently predicted an 11% rise in rapeseed output in 2013/14.
Isha Trivedi, an analyst at Phillip Commodities India Pvt Ltd., said crop damage made the rapeseed forecast look unlikely and predicted the rise could be more than halved to 5%.
India produced 6.85 million tonne of rapeseed in 2012/13 and was relying on a bumper crop in the year, ending October 31, 2014, to dampen imports of edible oils which cost it a record $11.3 billion last fiscal year.
Rajasthan state is the main producer of rapeseed.
"The rapeseed crop has been affected in Ajmer and Jaipur regions of Rajasthan. The early sown crop has been affected more than the late sown crop," said Dhiraj Singh, director at the Directorate of Rapeseed-Mustard Research, adding overall production would still be higher than last year.
In the 2012/13 marketing year ended October 31, edible oil imports surged to 10.4 million tonne, compared with 5.6 million tonne five years ago.
OTHER WINTER CROPS
Bhaskar Shinde was expecting to make Rs 500,000 from a bumper crop of chickpeas and red gram on the 18 acres he farms before hail and rains dashed his hopes.
"The crops were almost mature for harvesting. I could have harvested them, had rainfall come after two weeks," said Shinde, describing the damage as the worst he had seen in three decades.
In Madhya Pradesh, rain damage to chickpea and wheat was so extensive that the state government paid compensation to farmers, Shivraj Singh Chouhan, chief minister of Madhya Pradesh, said on Twitter.
"Everyone was expecting bumper production of chick peas, but unseasonal rains have spoiled prospects as the crop was in pod-filling stage," said Nitin Kalantri, a pulses miller based at Latur in Maharashtra, the second-largest pulses producing state.
Chickpeas are the main pulse consumed in India and the government was expecting a record output of 9.79 million tonne.
The benchmark April chickpea contract has firmed 8.6% in the last 10 days.
For wheat, the impact will be softened by massive stocks after years of bumper harvests. India had been expecting another record, at 95.6 million tonne, for 2014.
"In Madhya Pradesh and Uttar Pradesh crop damage is significant. I think the government will revise the wheat production number in its next estimate," said a dealer at a global trading firm, adding that rain would also delay harvesting in central India.
The government is trying to sell wheat overseas through three state-run traders, as the world's second-biggest producer attempts to cut huge stocks. A number of tenders have failed to reach the desired price, though Chicago wheat prices have risen to the highest since December on concerns over disruption in Ukraine's output and cold weather in the United States.
The potato crop had been damaged in Uttar Pradesh, said an official at the National Horticulture Research and Development Foundation.
Harvesting of potatoes, tomatoes and onions has started in some areas and the weather department is forecasting more rain in Maharashtra and Andhra Pradesh which could more damage.
