The first pilots at Port Phillip were licensed from 1839 with the Government taking over the service in 1853. Through the Act to amend the Act Intituled the Act to consolidate and amend the Law relating to Ports, Harbours and Shipping in the Colony of Victoria 1854 (17 Vict XXVIII), VA 4179 Pilot Board of Victoria was established to administer the service. The pilots were invited to purchase the three ships used for pilotage, form themselves into companies and take over the service on a cooperative basis with the Board responsible for the licensing of pilots, the making of rules and regulations for the service and the determination of rates of payment for pilotage. This supervisory function was transferred to VA 1424 Marine Board in 1888. Pilots received their own earnings with deductions for the support of the establishment and contributions to the Pilots Superannuation Fund.

Pilots operated in companies with a Secretary for each company responsible for the administration of the Company, the organisation of pilotage for ships and the reporting to the Pilots Board and Marine Board. Since 1971, all pilots belong to the Port Phillip Pilot Service with one of their number permanently in charge of the Williamstown Pilot Office as Secretary-Treasurer.

The major function of the Pilot Service is the expert pilotage of ships from Bass Strait to the Port of Melbourne and the Port of Geelong, particularly through The Rip at the entrance to Port Phillip Bay.