The MoD taking no risks in order to protect
staff and the general public.
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The work at Nancekuke, near Portreath, will mark the start of five dumping areas on the site being cleaned up.
Nancekuke produced about 20 tons of the nerve gas Sarin between 1951 and 1976.
Local residents are concerned toxic waste may have been left behind, but the MoD said land around the base was unlikely to be affected by chemicals.
Public protection
Nancekuke was a secret government base which operated as a small-scale chemical production and research facility between 1951 and 1976.
The base was closed in 1980 and turned into RAF Portreath.
Scientists began carrying out tests in 2003 to establish what sort of chemical substances were present at the dump site.
There were concerns that debris, such as test tubes, from the laboratories which made the deadly gases may have been dumped.
Although clean-up staff believe the area is safe, military officials have said they are taking no risks in order to protect staff and the general public.
The MoD said it hoped the clean-up operation would allay the fears of local people who have for many years been concerned about Nancekuke and its legacy.