First or all, to say that the practice causes suffering is not quite correct. Suffering can arise at any time. In vipassana, we are merely becoming aware of suffering when it occurs, and then we get to practice accepting it, allowing it, and letting it be. In this way, suffering becomes a teaching path that can lead us toward important insights about how the mind reacts to various stimuli, including physical pain.
It is not unusual to feel intense sensations of many kinds during our meditation practice. Pain is merely one of these events. Accepting that the pain is here, allowing it to be here, and and then letting the pain be can be a really insightful process, as long as we are not causing ourselves injury.
In Who Dies? An Investigation of Conscious Living and Conscious Dying by Stephen and Ondrea Levine, the subject of working with pain is given very detailed analysis:
It is important to recognize that there are various levels and intensities of pain. That all pains may not be able to be opened to with the same ease or perhaps even opened to at all. If we have waited until "the great pain" to open, it is quite possible that we will not have the spaciousness for deeper examination, because there has been so little preparation for such openness. But if we begin to play the edge of lesser pains, disappointments, fears, the wobblings of the mind, the contractions of the heart, in a gentle, day-to-day meeting and expansion, it prepares us for what comes later. It is the daily opening to the little pains that prepares us for the great pain. Playing the edge of our pain should be done with great compassion. Though it takes a certain steadfastness to maintain our concentration on, and openness to, pain, we should be aware of that quality of endurance that subtly creeps in to create some sense of a separate self with its accompanying resistance to life.Blessings,