The rain, which started in the middle of last week in the southern half of Henan, is causing some of the wheat to sprout or become affected by blight, according to videos posted on social media and a local grain dealer.
"Wheat is still unharvested and already sprouting," the dealer surnamed Li told Reuters on Monday.
China is expected to harvest a bumper crop this year, with officials estimating a crop at least as large as last year's.
The good outlook and a surge in imports in recent months has pressured prices in recent weeks to a one-year low, attracting demand from animal feed makers who are swapping corn for cheaper wheat.
However videos shared on China's Douyin platform showed water lying in fields around the city of Zhumadian, and blackened kernels of wheat, a sign of blight.
Wheat infected by Fusarium head blight cannot be fed to animals as it raises the risk of toxins, said Jan Cortenbach, technical manager at Wellhope Foods.
The rain is supporting prices to some extent, said Rosa Wang, an analyst at Shanghai-based JC Intelligence, though the full impact will not be clear until the rain ends.
The wheat price in Henan's capital Zhengzhou rose 2% last week to 2,740 yuan ($396.41) per tonne on Friday.
More rain is forecast for this weekend in western Henan, according to China's Meteorological Administration.
The Henan government has promised to help speed up the wheat harvest by facilitating transport of harvesters and drying equipment to farms, provincial newspaper the Henan Daily reported on Monday.
($1 = 6.9121 Chinese yuan renminbi)
(Reporting by Ningwei Qin and Dominique Patton; Editing by David Holmes)
