In the US, there is a difference. A clerk can be any type of subordinate employee who performs clerical tasks. For example, the shipping and receiving clerk files bills of lading, prepares shipping labels, and checks the manifests on incoming packages. But he doesn't have any real authority. A filing clerk maintains office files and probably reports to a secretary.
We don't use the term "secretary" very much anymore; that position is usually called an "administrative assistant." A secretary/Adm. Asst. usually has more education and experience than a clerk, and even though she may report to a supervisor or executive, she usually also has a certain amount of autonomy and authority. A secretary often makes decisions on behalf of her boss in his absence; a clerk does not.