Archbishop Chrysostomos on Thursday underwent spinal surgery and was recovering at a private clinic in Thessaloniki, the Church said.
A statement from the Archbishopric said the lumbar operation was successful and the 75-year-old primate was at the recovery stage.
The operation was carried out at Euromedica General Clinic by the team of Cypriot neurosurgeon Theologos Theologou.
This was the second such operation in around two years.
Chrysostomos underwent spinal surgery in October 2014 after feeling weakness in his right leg.