Black Sun Silver Moon(2001)

Taki thought he knew exactly what he was getting into when he accepted a job at the church as an assistant -- and he was mostly right, although the job description hadn't mentioned dealing with zombies! When night falls, the mysterious priest Shikimi and his new assistant venture into the graveyard to destroy the newly risen dead. The enigmatic priest always seems to know when and where these creatures will appear, and as the days go on, Taki begins to suspect that the danger may also come from within...

(Source: Go! Comi)