Clarence was protected as a Historic Shipwreck on 11 September 1985 under the Victorian Historic Shipwrecks Act 1981. Under Section 12(1) of the Act a 3.1 hectare protected zone was declared around the site. Activities such as boating, diving, snorkelling, fishing and anchoring were prohibited under Section 20 of the Act.
Today Clarence is protected by the provisions of the Victorian Heritage Act 1995 and lies within a 100 metre radius protected zone declared under Section 103 of the Victorian Heritage Act 1995. The protected zone was declared around the wreck site, prohibiting entry with out a permit. The zone was declared because any boats anchoring directly over the vessel could cause damage to the fragile hull; the site is also closed to SCUBA divers, fishing and snorkelling.
Provisions of the following Acts also apply:
- Commonwealth – Customs Act (1901)
- Commonwealth – Navigation Act (1912)
- Commonwealth – Protection of Movable Cultural Heritage Act (1986)