A method of operation of a secure programming system comprising a programming unit and a factory security system coupled to a programmer of the programming unit, the method comprising: reading, by the programmer, a silicon vendor device certificate from a programmable device mounted in the programmer; authenticating, by the factory security system, the silicon vendor device certificate using a silicon vendor public key; generating, by the factory security system, an OEM device certificate for the programmable device based on the silicon vendor device certificate, the OEM device certificate signed with an OEM private key; transferring, by the programmer, the OEM device certificate and a target payload to the programmable device mounted in the programmer, the target payload identified on a serial data list of device specific data to be programmed into the programable device, the OEM device certificate stored in a secure storage unit of the programmable device; extracting, by the programmer, the OEM device certificate and the silicon vendor device certificate from the programmable device after the OEM device certificate and the target payload are transferred into the programmable device; generating, by the factory security system, a validation status by authenticating the OEM device certificate of the programmable device using the OEM public key and authenticating the silicon vendor device certificate of the programmable device using the silicon vendor public key, the validation status set to invalid if the either the OEM device certificate or the silicon vendor device certificate are not successfully authenticated; and sorting, by the programmer, the programmable device into an output receptacle of the programmer based on the validation status. reading, by the programmer, a silicon vendor device certificate from a programmable device mounted in the programmer; authenticating, by the factory security system, the silicon vendor device certificate using a silicon vendor public key; generating, by the factory security system, an OEM device certificate for the programmable device based on the silicon vendor device certificate, the OEM device certificate signed with an OEM private key; transferring, by the programmer, the OEM device certificate and a target payload to the programmable device mounted in the programmer, the target payload identified on a serial data list of device specific data to be programmed into the programable device, the OEM device certificate stored in a secure storage unit of the programmable device; extracting, by the programmer, the OEM device certificate and the silicon vendor device certificate from the programmable device after the OEM device certificate and the target payload are transferred into the programmable device; generating, by the factory security system, a validation status by authenticating the OEM device certificate of the programmable device using the OEM public key and authenticating the silicon vendor device certificate of the programmable device using the silicon vendor public key, the validation status set to invalid if the either the OEM device certificate or the silicon vendor device certificate are not successfully authenticated; and sorting, by the programmer, the programmable device into an output receptacle of the programmer based on the validation status.