Complex sentence: It was the highest security Japanese Foreign Office system, but prior to Pearl Harbor carried little information about Japanese plans; the military, who were essentially determining foreign policy for Japan, distrusted the Foreign Office and left it "out of the loop".
Split into simpler sentences: It was the highest security Japanese Foreign Office system, but prior to Pearl Harbor carried little information about Japanese plans. The military, who were essentially determining foreign policy for Japan, distrusted the Foreign Office and left it "out of the loop".