Details of last Friday's incident have only just emerged.
Work at the site was halted this Friday afternoon to give all workers a refresher on health and safety.
Construction firm Morgan Sindall said it was conducting an internal investigation into the circumstances of the accident.
A spokesman for Aberdeen City Council added: "The responsibility for the site and the construction programme, as well as for reporting and investigating incidents, sits with the contractor Morgan Sindall Group.
"The health, safety and wellbeing of all those working on projects associated with Aberdeen City Council is of paramount importance to us and we will be kept informed by the contractor."
The Â£107m office, leisure and hotel development is due for completion in the summer.
Earlier this week, BBC Scotland revealed that only 10% of office space had been taken up for lease.
A worker was left with a fractured leg and ribs after an accident at the Marischal Square construction site in Aberdeen.