The incident came to light when members of the Seva Sahkari Samiti found doors of their office open when they went to the office yesterday, said SP Mithilesh Shukla.
He said that when police went inside the office they found locks of the cupboard, where Rs 20.42 lakh cash was kept, broken and the amount missing.
The cash was meant to purchase wheat, an office-bearer of Samiti said.
A case has been registered in this regard and further investigations are on.