1. You can not apply for reimbursement of salary to the ministry,
2. It is strange that you being a group 'A' officer of G.S.I. for last 4 years are not aware about how to calculate the salary or where to right in case there is a discrepency in your salary slip,
3. Write to your superior officer or salary paying department regarding the said salary discrepency,
4. For getting the payment of the bills for doing official work, get the said bills/expenditure approved by your sanctioning authority before sending the same for payment.