There are reconfirming decisions in the Australian Courts to show clear protection methods in this field. To understand the position there are two distinct elements to this question – Patentable Subject Matter and Medical Treatments.
Unlike the European approach, what is allowable or patentable subject matter of a patent is not prescriptive in Australia. Instead it relies on the Court determining the statutory interpretation of subsection 18 (1) of the Patents Act 1990 that:
an invention is a patentable invention for the purposes of a standard patent if the invention, so far as claimed in any claim:
(a) is a manner of manufacture within the meaning of section 6 of the Statute of Monopolies;
The interpretation of the effect of the historical Statute of Monopolies of 1623 on current Australian Patent law has had a long history. In 1959, the Australian High Court decided, in National Research Development Corporation v Commissioner of Patents  HCA 67,
…that a process to fall within the limits of patentability, must be one that offers some advantage which is material, in the sense that the process belongs to a useful art as distinct from a fine art—that its value to the country is in the field of economic endeavour.
The NRDC case involved a process of applying a herbicide to crops to eradicate weeds. The outcome of applying the herbicide was deemed to represent patentable subject matter on the basis that the economic effect of removing weeds from a crop was improved crop yield.
Since 1959, application of the NRDC decision by later Courts in determining patentability of methods of treatment of human beings, has brought varying results until now. In December 2013, the High Court of Australia in Apotex Pty Ltd v Sanofi-Aventis Australia Pty Ltd  HCA 30, affirmed by a majority judgement, that therapeutic treatment of human beings is suitable subject matter for a patent applying the NRDC principle of the treatment having ‘economic utility’ in the sense of a useful art as opposed to fine art.
In particular we can protect methods of medical treatment which involve therapeutic use of a pharmaceutical – some examples follow:
Apotex Pty Ltd v Sanofi-Aventis Australia Pty Ltd [2013 HCA 30] involved a patent (AU 670491 to Sanofi) having claims defining a treatment of psoriasis by administering an effective amount of a compound called ‘leflunomide’. Sanofi brought an infringement action against Apotex, and Apotex cross-claimed for invalidity of the patent. On appeal to the High Court, the only ground of invalidity relied upon by Apotex was whether treatments involving administration of therapeutic agents as satisfying the requirement of patentable subject matter.
The exclusion from patentability of methods of medical treatment represents an anomaly for which no clear and consistent foundation has been enunciated. Whatever views may have held in the past, methods of medical treatment, particularly the use of pharmaceutical drugs, cannot today be conceived as ‘essentially noneconomic’
From the Apotex decision, I believe the term ‘economic utility’ used in the context of the majority judgement refers to a therapeutic agent, drug, compound or composition containing an active agent, which when administered to a human being according to a dosing regimen, will have a positive outcome in the treatment of a diseased state. The economic outcome is not necessarily measured in terms of a patient’s ability to recover or resume work or contribute to the work force following the treatment (as asserted by the only dissenting judge), but in the production of the drug or compound in commercial quantities for sale. If this was not the case, i.e., a patent monopoly was not available for therapeutic treatments of diseased states such as Alzheimer’s disease, or asthma or psoriasis as in the present case, the rationale for pharma investing in research and development in therapeutic treatments, and the concomitant improvement is quality of life, would be adversely affected.
The High Court did however find a distinction between a method of medical treatment which involves therapeutic use of a pharmaceutical and the activities or procedures of doctors (and other medical staff) when physically treating patients such as surgery, which is considered non-economic and generally inconvenient. Hence doubt still remains for physical treatments such as surgical procedures.
The people at Baxter IP have a wide range of experiences in obtaining patent protection for medical treatments. If you wish assistance please contact me Warren Chandler at our Melbourne Office.