Cecil Clarke says Sydney is an ideally positioned, deepwater port capable of accommodating huge post-Panamax container vessels.
He says that puts it at a special advantage when it comes to trade with Europe.
Post-Panamax ships are vessels too large to fit through the Panama Canal, though that is expected to change once the expansion of the canal's lock system is complete next year.
Harper announced the trade agreement-in-principle Friday in Brussels, saying it should allow the free movement of goods, services, investment and labour.
The deal must still be approved by the provinces and the EU's 28 member states.