However, the supplies are expected to improve in coming days with rains receding in some parts helping transport of the crop to mandis.
The prices of tomato, the key kitchen staple, have gone up for last two weeks. It is available at Rs 75 per kg in Kolkata, Rs 70 in Delhi, Rs 60 in Chennai and Rs 59 in Mumbai, as per official data.
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"Frequent rains have not only damaged the tomato crop in big producing states like Karnataka, but also affected the transportation," Indian Council of Agricultural Research (ICAR) Deputy Director General (Horticulture) A K Singh told PTI.
According to reports from the states, the rains have started receding in Karnataka, giving some respite to growers and traders. The supplies from the state will begin to improve, he said.
In the case of Uttar Pradesh, the part close to Uttarakhand is still affected due to rains while the western region closer to Delhi is recovering. There are mixed reports from Madhya Pradesh.
Singh said it is difficult to access the extent of damage of the kharif crop at present. But these states have huge area under tomato crop and the supplies could not reach mandis due to poor infrastructure and transportation.
The country's tomato production is estimated to be higher by 15 per cent at 187 lakh tonnes in 2016-17 crop year (July- June), as per the government estimate.