There is no difference in rules regarding attendance for a Head Teacher, Assistant Teacher and Non Teaching Staffs.
There is an old G.O. (No. S/879 dated 10.11.1989) regarding Appointed Hour, Commencement of class teaching, Daily Assembly and Late Attendance of Staff in Schools which is equally applicable for teaching and non-teaching staffs.
Being the Head of the Institution he has no right to attend late in School, but this malpractice surely invite a false position for him.