A remote programming method is provided for safe and secure programming of a medical device at a remote location. A centralized programming instrument for use by a clinician or third party is provided with a network communication connection with a remote external medical device, such as a home programmer or monitor. The external medical device is located in the vicinity of a patient having an implantable medical device (IMD) and is in bi-directional telemetric communication with the IMD to allow instructions received from the centralized programming instrument to be transferred to the IMD. The remote programming method used for transferring information between the central programming instrument and an IMD includes measures to promote safe and secure remote programming of the IMD, which measures may include authorization requirements, programming condition requirements, implementation of programmed data requirements, and maintenance of a remote programming log.