Is a pharmacist's payment for medicine shortages at a government center considered Haram from government tickets?

The intent of the question is not precisely clear. However, if the aim is to address selling medicine and then finding a discrepancy between the sales price and the price at the end of the day, with the shortfall being covered by government vouchers, then you must inform the responsible authority of the incident so they can investigate the cause of the shortage. You are not liable as long as you have not been negligent in your work. If something else is intended, please clarify.