The operation will take place in the southwest and west of the country, the heart of the cocoa production belt, said Gneneyeri Sileu, in charge of plant protection strategy at the agriculture ministry.
The operation will cost 22 billion CFA francs (33.5 million euros, $40 million), he said.
Over the first three years, cacao trees will be ripped out -- the land will then be quarantined for a further two years to prevent the virus from bouncing back.
"In this particular context, there are no plans to systematically replant the 100,000 hectares," said Silue, who added that the operation would not have a major impact on national production.
Ivory Coast supplies two million tonnes of cocoa to the world market annually.
Cacao swollen shoot virus disease (CSSVD) is an insect-borne pathogen that typically affects a tree's harvest in the first year of production and then kills the tree within three or four years.
There is no treatment -- the only solution is to pull out and destroy infected trees.
The current outbreak was first recorded in 2004 in the central region of Marahoue, where it has destroyed more than 8,000 hectares, according to the National Centre of Agronomic Research.
CSSVD also affects neighbouring Ghana, the world's number two producer, where it was first discovered in 1936.
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