The exact number of insects involved is still being evaluated but KWS spokesperson Paul Udoto told the BBC this was the country's first case of "bio-piracy" on this scale.
The four suspects – two Belgians, a Vietnamese and a Kenyan – were arrested after what the KWS has described as "a co-ordinated, intelligence-led operation".
It is believed that the intended destinations were the exotic pet markets in Europe and Asia.
The KWS said the demand for rare insect species is growing. Collectors keep them in special habitats, known as formicariums, and watch them build their colonies.
The giant African harvester ant - or Messor cephalotes - is the largest of its species and can grow to around 20mm, with the queen growing up to 25mm.
Pat Stanchev, the general manager of insect-dealing website Best Ants UK, said that it is their "big and beautiful size" that makes them attractive for those who want to keep them as pets.
He does not sell the giant African harvester ant but told the BBC that he is aware of people who try to pass on illegally imported insects.
In Kenya, the ants are protected by international bio-diversity treaties and their trade is highly regulated.
"This prosecution sends a strong message that Kenya will enforce compliance… and marks a significant step forward in Kenya's fight against unconventional wildlife crimes," the KWS said.
The four men are due to be sentenced on Tuesday.
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