This is gonna sound really harsh.
First of all, I can tell this has a lot more effort put in to it than a lot of flashes I've seen on Newgrounds. For one, they fighters aren't sticks. Another point of interest is that the "camera" angle actually changes, and isn't static. The sound effects were synced well, also.
That being said, there isn't a whole lot that goes on in terms of story. The characters' only motivation is to just kill each other? Can't the ninja just have a target and the samurai is protecting him/her, maybe? What many artists on Newgrounds do is substitute story for a lot of action. But this fight was rather short, and the animation wasn't mind-blowing. Believe me when I say that I know a lot of work went in to what you already did, but it just seems unfinished to me.
The footstep sound effects were synced, but not varied enough, and became tedious. The action was a little hard to keep up with due to the animation not being as smooth as it could be.
The music, while good on its own, did not really compliment your work very well in my opinion. But at least you used music.
Overall, you have a lot of potential. You just need to dedicate a little bit more time into this project, and it could be amazing.
On a final, ending note: Samurai killed ninja all the time back in their time of existence. Everyone who's asking how it happened, or saying its impossible should look up some history. Just because anime and other fiction likes to show ninja as being superior... truth is that there are no recorded successful assassinations made by a ninja.