The rain, otherwise a welcome respite from heat, is feared to have damaged hundreds of sacks of tur daal on the premises of agriculture produce market committee at Wardha in Vidarbha.
The sacks were stored out in the open, said a district official.
Elsewhere, pre-monsoon showers lashed the coastal areas including Amboli, Sawantwadi, Kudal and Vengurla.
Rain accompanied by thunderstorm was reported from Sangli and some other places in western Maharashtra too, Met department said.
Parts of Beed district in Marathwada received heavy showers late last night.