A number of Commonwealth agencies are not subject to the legislation at all and several others are excluded for certain types of documents (for example, documents concerning the competitive commercial activities of the particular agency). Exclusions are set out in Schedule to the Act. Several of the exempt agencies are engaged in commercial operations (such as CSIRO). Other organisations which have been excluded from the Act are concerned with matters such as Aboriginal self management, labour relations and Australian secret intelligence (for example, the Australian Security Intelligence Organisation and the Australian Security Intelligence Service).

Twenty agencies currently have exemptions for particular classes of documents, mainly relating to the agency's competitive commercial activities. These agencies (for example, the Commonwealth Attorney-General's Department, the Australian Postal Corporation and the Federal Airports Corporation) have had documents excluded as they would be significantly disadvantaged in their competition with private sector organisations who could obtain information about their operations through FOI legislation. Examples of other classes of documents that are protected include Australian Broadcasting Corporation and SBS program material. See Schedule 2 of the Freedom of Information Act.