Well, (because I was know a lot of firearms) there's several possibility:
1. The sniper use a larger caliber weapon than 7.62x51 NATO or 7.62x54R (Possibly).
2. Elevation. Because the target's location (Tokyo Tower) was different than the sniper's location.
3. I was curious why he didn't use suppressor (or silencer in the case...) on his weapon.
On this video, we can explain about the trajectory of the bullets (and range...).
http://www.youtube.com/watch?v=V8erXeE_4O4