I have resigned my job.As per my appointment i can pay 3 m salary in lieu of 90 days notice. I am not relieved

In terms of your appointment order you should either give 90days notice or 90 days pay in lieu of notice. I understand your management has subsequently relaxed and made it discretionary on this stipulation. You have given 15days notice and your management is using their discretionary power in not relieving you from the job. Management has within their power not to relieve you, they do not want to use the discretionary power in your favour. It shows that you do not have good rapport with the management. Normally management would not like to block any body's exit. Best thing for you would be to pay 90 days salary and get relieved. As it is not a punishment management cannot deprive you of your statutory terminal benefits.