Mate of mine wears contact lens and did so through training even though the official answer is no. They will give you some army issue glasses but these will take a few weeks to arrive and will make you look like Joe 90 or Michael Cain as Harry Palmer apparently. If they do let you, or turn a blind eye so to speak, then the month long continuous wear are probably best cause taking them out and cleaning them on exercise will be a nightmare, both because of time constraints and dirt. Oh and obviously he didn't wear them through NBC training as the gas is liable to remain on the lenses in your eye and will not do you much good.
I'm reliably informed that you can wear them after phase one with no problems.