We usually use the idiom to represend a problem of finding something. Your office is untidy and you can't find a particular document: it's like looking for a needle in a haystack. I'd be wary of using it just to represent a difficult task in general, because it's an image designed to evoke difficulty in finding something.The mission is as difficult as looking for a needle in a haystack.
Does this sentence sound good? I mean, is it a good comparison?