I recently bought a MPU6050 acc/gyro from http://www.w11stop.com/sensors/accelero ... -gyrometer. I have previously used this sensor with arduino uno and it worked fine but now m using it with arduino due. Since arduino due works at 3.3V logic level unlike arduino uno which works at 5v level. Will this make any difference on the functionality of the mpu6050 sensor?

No, but maby you need to use voltage level conversions.
Look at this:
http://mirekk36.blogspot.com/2015/05/konwerter-poziomow-33v-ttl.html

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In Arduino Due You don't have to use any logic level converter. Both are working on 3,3V logic level.

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