There are two ways I have seen:
1) A person is using a treasure map and uncovers a sealed ninja. The system sends out a worldwide announcement saying (insert username here) was not being careful when digging with a treasure map and uncovered a sealed ninja. Quickly seal him" or something along those lines.
2) Sealed ninjas randomly appear and are announced by the system. Eh. . .

And yes, to the people above. The sealed ninja can give seal scrolls. . . I think Scionstorm got one from a sealed ninja battle in his recent video.