Last week fencing around the domes was removed, and the first radome covering was lifted off on Monday morning.
In November, it was announced that the decision to retire and remove the radomes and dishes had been made.
Dish use had become virtually "obsolete" after changes in global telecommunications and information technology.
Hampton said while the dishes and the radomes are no longer in use, the GCSB said the Waihopai Station will continue to operate.
"More modern and proportional methods collect more targeted communications, and these other forms of intelligence collection are now more effective and efficient at contributing to the Government's National Security and Intelligence Priorities than this type of satellite communication interception undertaken at Waihopai," Hampton said.