How to deal with body pain during meditation?

Your body must get adapted to prolonged sitting. Your discomfort will cease with practice. Exercise if your body is not in a good shape. Eat adequately and drink enough fluids.

When pain arises during your meditation, observe it and learn from it. See its impermanence. See as much as you can. Then, let go of it by moving your mind's focus on a different meditation object and notice how pain ceased. If pain arises again, repeat the process - observe the pain, then let go by moving your mind's focus on a different meditation object.

With time and practice, either your pain will subside or you'll learn to non perceive it, and you'll be able to sit still in your meditations without distractions from pain.

Prevent body pain by being limber and strong through Hatha Yoga. That is why it was developed! If sitting hurts, you are doing it too much throughout the day, or you are not stretching and limbering... throughout the day. At my workplace I take walks outside on the morning and afternoon breaks and at lunch. On those walks I stop at benches to do an assortment of stretches that I have learnt over the years. You cannot do it just once a day and not move the rest of the time.

The body has needs, among which are to be used properly, exercised and stretched properly, and rested properly. These amount to laws of physics and cannot be ignored. There is no point whatsoever in denying your body to try to 'progress' faster spiritually. It is just as useless as not stopping driving your car to get more fuel, oil or whatever to "arrive sooner". No. You will arrive at the side of the road with a disabled car.

I used to do lots of walking and stretching, and yes, often I would tense up after an hour or so of sitting meditation, but with the right exercise and a very good seat (such as I used to build and sell) You can sit much longer on "good days". Take care of yourself.

There are quite a few things to consider here to become skillful at approaching pain and discomfort during practice.

Most people experience discomfort and pain in meditation from time to time - so don't let this get you down :) The body (or the mind ;) is not used to sitting still for too long and will complain in some form or another. This is balanced on the other hand by wisdom that in some situations the body complains for a reason and that perhaps you need to adjust how you sit.

In your instance I don't know if you're using a cushion ... if not, sitting cross legged style without support puts stress on the pelvis and creates pressure on the legs where they connect because of the weight of the legs. You have to (1) raise your buttocks with the aid of a cushion or zafu (2) provide support under your knees with smaller cushions if you are not flexible. Another option is a meditation bench.

"If ... we simply generate the three primary gestures of alignment (the pelvis higher than the knees; the very bottom, or even a place just in front of the very bottom, of the sitting bones contacting the cushion; the upper torso balancing itself as effortlessly as possible over the stable base of support created by the first two gestures) and then allow the body to make whatever adjustments in posture spontaneously occur, the feeling tone of alignment gradually and inevitably begins to emerge. Paying more attention to the feeling tone of alignment rather than its spatial coordinates allows us to align ourselves with gravity from the inside out." - Will Johnson, The Posture of Meditation

... after you have done the above preparations listen to Shinzen Young:

When you sit and meditate you may sometimes be subject to discomforts, aches and pains, sleepiness, body sensations of agitation and impatience, itches and awkwardness from the posture. These discomforts are real but quite manageable. In the meditative state you can experience them with more mindfulness and equanimity than you would in daily life. As a result the mind and body go through a natural change, a deep learning process that affects the unconscious levels of neural processing ....True asceticism is a delicate skillful process that uses pain to overcome pain. When properly understood and practiced, it deepens our humanity, elevates our satisfaction with life and break up blockages in the deep reaches of the mind. When improperly understood, asceticism ceases to be delicate and skillful and degenerates into something pathological. One pathology is extremism, which can end up harming the body and weakening mental focus. A second pathology is spiritual macho, seeing how tough you can get. A third pathology is spiritual masochism, exposing yourself to discomfort because you consider yourself to be a worthless worm who deserves to suffer. Spiritual machismo and spiritual masochism both subtly reinforce a fixated ego; on the other hand, authentic asceticism shows us how to become free from the suffering self.

In principle, many contemplations that are part of satipatthana don't require our bodies to be still. In fact, a good portion of it are "24/7" practices to be developed whatever we are doing wherever we are.

On the other hand, all of these practices are immensely helped by concentration¹ -- thus, the satipatthana sutta opens with concentration practice (calming of the breath). And some, I think, are particularly hard to do (that is, severely limited) without some degree of concentration. And concentration is hard (or seemly impossible) to develop in the presence of significant body discomfort.

Therefore, ideally, it's quite important to have a practice without discomfort. And here it's important to remember that, ultimately, the body form has little to do with the actual work: what is important is not the form, but if the posture (whatever it is) enables the practice.

There is the possibility that the pain from sitting in a certain posture is temporary and will not be an obstacle after a while. But there is the possibility that every sitting will be unbearable after a few minutes or a an hour or two (I meditate for over 15 years, and still can't sit cross legged for more than 30 minutes without discomfort, let alone ~2 hours -- which I've done twice in the past, enduring excruciating pain).

For this last case, if your sitting is of 20 minutes, 1 hour or 4+ hours, I think the best long term solution for practicing is to find out a posture where your body can be still and rest comfortably for the desired period while your mind is alert. Finding out a solution may involve trying out cushions and leg positions, exercises, or entirely different alternatives (e.g meditating laid down or in a chair).

¹ a.k.a: tranquility, samatha, samadhi, jhana practice.