Until the nineteenth century, ships arriving from plague infected areas had been subject to quarantine, but this proved ineffective in controlling the spread of cholera.

On the premise that preventing epidemics would reduce the local expense of providing for paupers, the General Board of Health commenced in 1849 to issue provisional Orders assigning to the Poor Law Guardians power to deal with ships suspected of having cholera on board. This resulted in a conflict with the Commissioners of Customs, who had responsibility for the administration of quarantine but the General Board of Health had the support of the burgeoning shipping interests. As quarantine was counted from the departure of a vessel from a cholera infected port, this was to the disadvantage of steamships in which Britain had a lead.

In 1866 the Sanitary Act made ships subject to the jurisdiction of the Nuisance Authority, but as many ports extended over the area of more than one riparian authority the Public Health Act 1872 provided for the establishment of one Port Sanitary Authority for each Customs Port. Following the repeal of the 1825 Quarantine Act, the Local Government Board took over from Customs the health control of shipping.

The costs of providing isolation hospitals became a charge on local authorities, and the Association of Port Sanitary Authorities was constituted in 1899 with the primary objective of obtaining exchequer support for this service. Eventually a 50% grant for approved expenditure was conceded by the Local Government Board, and this was paid until the re-organisation of local government in 1974.

The Association became involved in the introduction of Imported Food Regulations in 1908, and actively supported better conditions aboard ships for merchant seamen.

With the development of commercial flying, the Association became involved in the health control of aircraft and for a number of years was known as the Association of Sea and Air Port Health Authorities. The Association now has over 50 members and strives to be the lead agency in promoting port health in the UK.