Shakotan, is considered a very safe destination for solo female travelers. The crime rate is incredibly low and the locals are very hospitable. You will feel warmly welcomed and respected in Shakotan. Just make sure, as in any city, to use common sense. This includes not walking alone at night in less crowded areas and informing someone about your whereabouts. Also, Japanese people highly respect privacy which means you'll feel comfortable and safe during your visit.