Many thanks to Matthew and Dan for providing references to where the Bodhisattva-bhūmi describes situations in which a bodhisattva may perform an act such as killing, which is otherwise prohibited by the Buddhist precepts. In the new English translation by Artemus Engle these can be found on pp. 276-282.

I had heard the story from the Buddhist Jātakas of a ship captain who killed a robber on board his ship. The captain was actually a bodhisattva, who with his infallible prevision knew that the robber would kill all 500 of the merchants on board the ship. So to prevent this, and to prevent the awful karma that the robber would generate by doing this, the bodhisattva captain out of compassion took upon himself the negative karma of killing and killed the robber.