Payment of salary is traditionally by cheque only. Now a days, even payment as low as Rs. 5,000/= or so is being made by cheque. There is a circular of the government that any payment beyond Rs. 20,000/= has to made by cheque. Further, you save a lot of hassles by making payment by cheque. However, the company can make payment less than Rs.20,000/= by cash also. All depends on the company's policy.