A secret key is programmed into a key transponder from a base station wherein the key transponder stores a fixed ID, a first default key segment stored in a first memory page, and a second default key segment stored in a second memory page. The secret key comprises a first new secret key segment to be stored in the first memory page of the key transponder and a second new secret key segment to be stored in the second memory page of the key transponder. A mutual authentication process is initially conducted using the default key. Write commands are sent to the key transponder in transferring each key segment. Write acknowledgement signals and confirmatory reading back of the data are employed for ensuring proper storage of the secret key. Recovery from the most probable types of errors enables successful programming of key transponders in an efficient manner with a low loss rate.