She said in the run up to the GST, pharmaceutical firms have taken a huge hit on their businesses in June as a result of pharmacists declining to keep stock.
"Our stockists are refusing to stock, the supply chain is also not willing to accept material," Mazumdar-Shaw told television channel CNBCTV18.
Commenting on the possible fallout, she said: "I think bigger impact is the drug shortage that patients are going to face and then we are going to have huge impact on price of drug."
"Pharmacies are not willing to stock medicines...Many of them said they are not prepared for GST that is very scary," she said.
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While the companies are prepared but the rest of the supply chain is not prepared, she said adding there were very nervous and worrying signs from pharmacists, stockists and pharma supply chain.
"They are not even prepared of their IT backbone and required IT capability to deal with GST. Lot of them are saying that formalities involved are so complex that they are really worried whether they can cope with it," she said.
While Biocon's business is very small in domestic market but those pharma companies which are totally dependent on domestic market are seriously impacted, Mazumdar-Shaw said.
She lashed out at the GST in its current form saying it has been made into a multiple and complex tax regime and criticised the GST panel for doing "a suboptimal job of delivering a game changing GST regime".