The work, part of a £2.74 million refurbishment, is being monitored by Perth firm Alder Archaeology Ltd.
Despite planning to reduce excavation and disturbance below ground, the discovery of human remains was anticipated.
The limited excavations have also revealed the medieval wall foundations, traces of a wooden floor and a small Victorian cellar.
St John’s has been Perth’s parish church since at least 1120, if not a century earlier. After the Reformation it was divided into the east, middle and west kirks, but re-united and restored by Sir Robert Lorimer in 1923.
The church has been adapted and remodelled many times over the centuries and it is thought these renovations will uncover further traces of the previous changes.
The current programme of renovations and repairs, under the title of Vision For The Future, aims to improve access, seating and heating, and versatility of use.
Much of Perth’s medieval population is buried in and around the building.
Although burial in the kirk was prohibited after the Reformation, it continued into the 17th century and many graves were disturbed during the Lorimer restoration.
Remains found will be carefully recorded and reburied in due course.
So far only scattered remains reburied by Lorimer have been lifted but some undisturbed burials have also been found.
The new heating system is being repositioned to ensure they remain undisturbed, and prior to the remains being re-covered, the Rev Jim Wallace conducted a short service of prayers and readings for the re-committal.
A revelation has been a tiny flint scraper found under the floor.
David Bowler of Alder Archaeology said, “Perth sits on a small, dry platform overlooking the crossing of the Tay. It would have been an important site in prehistoric times, but the evidence is deeply buried under medieval Perth and rarely seen.
“It is exciting to find a prehistoric tool right in the heart of the medieval burgh, in the first week of excavation.”
Sarah Winlow, heritage officer at Perth and Kinross Heritage Trust, who have a monitoring role over the archaeological works, said, “It is good that the project team has taken on board the significance of the medieval archaeology within the kirk, quickly reacting to any discoveries and adapting design to ensure there is little disturbance to these important deposits.”
The major work began towards the end of August and the kirk, widely regarded as Perth’s most important building, will remain closed until April.
Source: The Courier