Forensically he has been involved operationally throughout the UK in over 200 homicides, has also worked in Bosnia, Serbia, Kosovo, Iraq and the Falklands and routinely lectures to police and forensic professionals. He helped found the Forensic Search Advisory Group, was a lead assessor for the former Council for the Registration of Forensic Practitioners (CRFP), and was primary in setting up the current validation system for forensic archaeology within the Chartered Institute for Archaeologists. He currently chairs the Expert Panel of Forensic Archaeologists
John Hunter was also a Royal Commissioner on the Ancient and Historical Monuments of Scotland, is an appointee of the Cathedral Fabrics Commission for England at Worcester Cathedral and sits on the National History Museum Scientific Advisory Panel (human remains). His most recent interests, however, concern landscapes and social change in Scottish islands.