Kindly enlighten :

Company "X" is buying items from its own employees cooperative society and paying VAT. Member employees are also paying VAT and thus actual purchase price is much higher if one buys from Cooperative instead from Market Retail. Objective of cheaper goods gets lost.is there any way out? Since VAT amount is small, mostly company "X" misses out VAT credit.

The option available to Company 'x' is to buy the item from the market itself. Secondly since employee cooperative society is part of the company, you can forward your monthly requisition to the society, so when they place their order, your items are separately included in their purchase order, whereby the company has the privilege to settle the payment separately to the vendor. This process may help you to reduce your cost burden.

If the goods purchased and paid vat in appropriate rate then no one have legal right to ask the company, There is big difference between company employee and employee a part in soicety.  Buying and selling is in their own wish . If you need more depth then need more details

I do agree