The conditions aboard vessels could lead to public health hazards for crew and passengers. The International Health Regulations provide for six monthly inspections of all ships engaged in international trade to ensure that vessels are free of pests and food is prepared and stored hygienically. Water supplies to ships and aboard vessels are also monitored. In circumstances that pose an imminent risk to health, PHAs work with the Maritime and Coastguard Agency to detain the ship until remedial measures have been taken.

A major function at the larger ports is the control of products of animal origin and foodstuffs imported from countries outside the EU. All such commodities are liable to inspection by PHA's, and products of animal origin undergo at least a documentary check on the health certificates that have to accompany each consignment. More detailed checks are carried out at dedicated inspection facilities that have to be approved by the European Commission.

PHAs are responsible for some pollution control measures within ports such as dust and dark smoke emission and ensuring certain processes, such as cement handling do not cause pollution. PHAs are also responsible for enforcing the new smoke free legislation in ports.