Contray to popular belief, the ninjas' sword did not have any kind of specific design. The straight-blade, square tsuba swords are a product of hollywood.
The actual ninja sword looked just like the samurai's daito or katana, but with a few small exceptions. For one, they were usually of a much poorer quality. To a samurai, his sword was his life. To the ninja, it was an important weapon, but not so important that it couldn't be replaced if broken or lost.
There is some conflict in history as to whether ninja were formidable swordsmen. This is because there were so many different clans and groups of ninja, it is quite possible that some were well trained in the art of the sword and others were not. Since the ninja were warriors and soldiers alongside the samurai, in everyday life they had to appear as a normal soldier. Having a sword of a unique or special design would identify him as a ninja. This would cause problems, because ninja were always suspect!
Sometimes the ninja would carry a sword whose blade was slightly shorter than the saya in which it was carried. The additional space would be used to hide blinding powder. Also some ninja would have a removable end piece on the saya so it could be used as a snorkel or filled with muddy water to be used as a type of metsubushi. Metsubushi is anything which blinds an enemy.
The ninja sword also had a slightly longer sageo than the samurai sword. This was so the ninja could carry the sword by clenching the sageo in his teeth while climbing.