This problem might have a few reasons - position of the knees, practice tempo, and position of the feet. Let me discuss each of them in turn:
Turning the knees to the direction of the notes being played is critical, because otherwise there is some danger of damaging your knees if you don't. You see, if you play in the lower regions of the pedalboard but your knees are facing right, you will start to feel tension and pain in your knees. Likewise, keeping the knees facing left but playing on the right side will cause similar problems.
Practice tempo when playing pedal scales should be extremely slow at first. Basically, as you play each note try to feel and check if your body is relaxed or not. Breath deeply and slowly, if you need to.
Position of the feet is important because sometimes the left foot should go under the right and sometimes above the right. It depends on whether you are playing white notes or sharp notes. Keep the heels together and press the pedals with the inside portion of your feet (big toe).
Keep these points in mind when practicing scales on the pedals and it will help you avoid the tension in your upper body. In time you will gain special flexibility of the ankles which is the basis for playing scalar passages with pedals.
What about you? Do you feel tension in your body when performing pedal passages?