The league confirmed on Tuesday that six people from three different clubs had tested positive for the novel coronavirus.
Chelsea FC are now in fourth place in the Premier League table as they chase a top-four finish in Frank Lampard's first campaign in charge.More news: Seahawks' offer to running back Devonta Freeman was worth up to $4M
Kante caused concern among team-mates in 2018 when he fainted after a training session; his brother died of a heart attack the same year.
Troy Deeney and Danny Rose have also expressed concerns about returning to training with data from the Office of National Statistics suggesting black men and women are nearly twice as likely to die from coronavirus compared to white men and women.
The 29-year-old will now train at home and the club will continue their efforts to make their training ground safe for the rest of their squad.More news: Universal Orlando Wants to Reopen on June 5
Telegraph Sport revealed this week that Kante was granted compassionate leave to miss training because of his concerns over the safety of returning to football.
Kante's decision follows a similar stance taken by Watford captain Troy Deeney.
Chelsea have seen several other previously injured players come back after being out before the shutdown, including the likes of Abraham, Mateo Kovacic and Christian Pulisic.More news: Updated COVID-19 Case and Death Numbers For Los Angeles County
Midfielder Kante is understood to have mostly remained indoors with one of his brothers since the suspension of the Premier League season on 13 March.