Well, the way I see it you only have one solution and that requires..., lots of machine guns, attack trained hyenas, motion sensors, trip wires, incredibly complex password systems that are updated on an hourly basis, seventeen chainsaws, plutonium, large quantities of hallucinogenic smoke grenades and a slinky.
After you acquire all of these items get back to me for further instructions. We'll take care of that damn ninja. Trust me, I have a seventy five percent record of successfully dealing with Ninjas.