Ministry of Health Director-General Doctor Patrick Amoth made the announcement on Wednesday.
He further explained the variant was detected in 71% of the 1277 samples collected between March 2020 and April 2021.
Additionally, Amoth says five people in Kisumu are currently being monitored for the strain.
He spoke on the day 489 people tested positive for Covid-19 bringing the total number of confirmed cases to 161,393.
The health official stressed that Covid-19 cases had significantly reduced with the positivity rate currently at 11 percent.
The Indian variant that has a mutation similar to the one found in the South African variant is believed to be driving the second wave in India.
Deaths in India have already surpassed the 200,000 mark with at least 300,000 cases being reported every day in the past week.
President Uhuru Kenyatta recently had to lock down five counties due to the high infection rates that were recorded in the area.
Nairobi, Kajiado, Machakos, Kiambu and Nakuru were identified as red zones. However, he later lifted the cessation of movement in the five counties saying that the COVID caseload within the zoned area has come down by 72 percent.
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