Last week, the government had brought down import duty on wheat to zero from 15 per cent to boost domestic supplies and control rising prices.
Food Corporation of India (FCI) is the Centre's nodal agency involved in procurement and distribution of foodgrains.
"The decision (to scrap wheat import duty) has been taken by the government taking into account the entire situation prevailing in the country. It will not impact sowing. It will not affect farmers as wheat is normally purchased by the FCI," Pattanayak told PTI.
FCI had procured about 23 million tonnes of wheat in 2015-16 and 28 million tonnes in the previous year, he added.
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Asked if the Agriculture Ministry had opposed the decision to allow duty-free wheat import, the Secretary said, "I cannot say at my level. Please ask the minister because he is the highest authority who decides. It is not our decision."
"Basically, the analysis has thrown up one thing that there was zero import duty from 2006 till 2015. In was only in 2015, the duty was reimposed. India wanted to go back to the earlier regime. Nothing much to be read into that," he said.
There has been brisk sowing of wheat, the main rabi (winter) crop, so far even as the Met Department has projected warmer winter, and experts have warned about production loss if temperature rises in crucial February-March period.
The country had harvested 93.50 million tonnes of wheat in the 2015-16 crop year (July-June), much higher than the industry's estimate of 86 million tonnes for the same period.
However for this year, the Agriculture Ministry has kept a target to achieve record 96.50 million tonnes of wheat.