"A case of circulating vaccine-derived poliovirus type 2 (cVDPV2) has been confirmed in Bamako," WHO said in a statement.
Mali authorities had detected polio in a 19-month-old child from Guinea, who was brought to Bamako for medical treatment seven days after paralysis set in on July 20, the UN health agency said.
There was a case of wild poliovirus in Mali in June 2011 in the Timbuktu region.
The announcement today came less than a month after Africa marked one year since the last recorded case of wild polio, which raised hopes the continent was moving towards eradicating the crippling disease that usually impacts young children.
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Two polio cases confirmed in Ukraine last week were also due to a type of vaccine-derived poliovirus.
Vaccine-derived polio infections are in rare cases caused by one type of polio vaccine, which contains small amounts of weakened but live polio virus.
Oral polio vaccine (OPV) replicates in the gut and can be passed to others through faecal-contaminated water, thus imperilling unvaccinated children.
The latest case is genetically linked to a confirmed case of the virus detected in the Siguiri district, in the Kankan Region of Guinea, in August 2014, which appears to have been circulating undetected across international borders for more than two years, WHO said.
"The risk of spread of this virus is deemed high and it has the capacity to cause paralytic disease in humans or kill," the agency said, warning that the emergence of the virus revealed "low population immunity against the virus due to low rates of vaccination coverage in Guinea.