Government Communications Security Bureau director-general Andrew Hampton said the domes have been deflated and lifted off by crane and the steel antennae will now be dismantled in sections.
Once removed, the dish and dome materials will be safely disposed and the steel scrapped.
In November, the GCSB announced the decision to retire and remove the radomes and dishes after more than 30 years of service, saying the technology at the station is now virtually obsolete.
It said at the time that in the past year less than 0.5 per cent of intelligence reports GCSB produced were based on the interception of satellite communications by Waihōpai, and funding can be more usefully invested in other intelligence capabilities.
Hampton said the GCSB needs to continuously assess and update its capabilities to ensure they contribute to the fullest extent possible to the government's priorities, as well as respond to rapidly evolving technology, and to the security threats New Zealand faces.
The first of the two 18-metre diameter dishes and radomes was constructed and began operating in 1989, with a second dish and radome added in 1998.
The station has attracted protest action with activists breaking in and deflating one of the domes in 2008. They were charged with causing intentional damage but later eventually acquitted.
While the dishes and the radomes are no longer in use, the Waihōpai Station will continue to operate and support the GCSB's ongoing national security activities.
