The medical department was a science department aboard the USS Enterprise incorporating doctors and medics.

After the M-113 creature infiltrated the Enterprise, Uhura declared a medical department alert, asking doctors and medics to acknowledge. (TOS: "The Man Trap")

After Leonard McCoy overdosed on cordrazine, captain Kirk lamented that the medical department knew as little as he did. (TOS: "The City on the Edge of Forever")

During the 2267 crisis on Deneva, Kirk requested analysis by the medical and life sciences departments. (TOS: "Operation -- Annihilate!")

It seems that the ship's doctor might not be the department head of the medical department, as in "Where No Man Has Gone Before" Mark Piper identified himself as the head of the life sciences department instead, and "Dagger of the Mind" implied that McCoy had a single department.
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