Hi, I'm using JTAPI for Consult and Conference. During that time customer hears a static beep sound for few second..

The Flow as below

Customer -->IVR --> Agent
Agent click Authentication button , it invoke JTAPI application which will Consult the current call with IVR and Complete conference .

The Customer hear a beep sound for few seconds (1 or 2 second) and hear IVR

I am assuming you are intersted in the source of that beep?

There is a Communication Manager feature that will play a tone when a call is conferenced.
See "conference Tone"

https://documentation.avaya.com/bundle/AvayaCommunicationManagerScreenReference_r7.1.3/page/systemParametersFeaturesP6.html

I would assume they hear it anytime a call is conferenced.
If not, does it occur if you manyally conference the IVR into the call?
Does it occur if you conference in another station?

Start isolating when the tone occurs and when it doesn't and investigage Communication Manager tones for that scenario. Alternatively the tone may be part of the IVR script.