Normally, a company secretary will work most closely with, and report to, the chairman of the board. However, it is good practice for ultimate authority over the secretary to lie with the board of directors as a whole, rather than any individual director. For example, any decision to remove the company secretary from office should be taken by the board as a whole.
This is because a company secretary has a role in providing impartial advice and ensuring that the company is properly governed by the board. This could be compromised if the chairman (or some other director) can exert undue influence on them.