Recently I have worked with arduino uno and mega2560 with MPU6050 http://www.w11stop.com/sensors/accelero … -gyrometer and it worked fine but now i am using it with arduino due. Since due works at 3.3V logic level so will it be a problem for the sensor as well to work because uno and mega works at 5V logic level unlike arduino due??
The MPU6050 datasheet clearly states that it is a 3.3 volt device. (Even the link you gave) So there is no reason to think it should not work with a 3.3 volt DUE.
BUT! If the 5 volt Arduino Uno and Mega already damaged it then who knows how it is going to work at 3.3 volt. Absolute maximum ratings are 6 volts. Maybe it worked and seems fine initially at 5 volts. Over time the 5 volts may have degraded it’s sensitivity and damaged it.