Item is found shortage in Store at the time of physical counting then who will be responsible for this shortage?

warehouse or inventory management department

WH Team

Direct responsiblities goes to the warehosue Incharge and indirectly  accounts, logistics is also responsible for such variation in the stocks

Warehouse Manager , But in between the accounting sections take share as the head office MUST always be in touch with the warhouse to know the movment of all items to reduce any lose can take palce , by sequence make internal control.

iNVENTORY MANAGEMENT(OR) MATERIAL MANAGEMENT

Inventory Manager is primarily responsible but it should be traced as when and how it happened. Could be due to data entry error also.

Primary responsibility is of the warehouse manager followed by the commodity incharge. I dont think accounts has any role toplay in this except at the end ( Project/ Year) when the inventory is done.

If the count on the system was verified to be correct (no erroneous trnsactions are recorded for the item), then the warehouse manager is responsible for the differentce, otherwise it either the system's user(s) or the system itself.

warehouse team 

Item is found shortage in Store at the time of physical counting then Store Manager or Wharehouse Manager will be responsible for this shortage