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Thipe and Rapula Sefenyatso, who has also tested positive, are the latest among 10 SA athletes who have failed tests for banned substances this season.
Thipe tested positive at the African Athletics Championships in Benin in June and Sefenyatso, a promising men's 200 metres specialist, tested positive at the Yellow Pages Meeting in Pretoria in April.
"I don't know what is going on, but doping in South African athletics is becoming a serious problem," said ASA president James Evans.
"To have 10 athletes testing positive in a season is just not acceptable.
"South Africa seems to have some of the dumbest athletes. They know that they will be caught, but they keep on using banned substances and making the same mistakes over and over again."
Thipe was the first black woman to represent South Africa on the track at the Olympics when she competed in the 400m event at the Beijing Games in 2008.
Perhaps the country's most versatile sprinter, Thipe won the women's 100m and 400m events at the 2009 SA Athletics Championships in Stellenbosch.
She then took time off from the sport for the birth of her first child but made a comeback this past season.
Bursting back in stunning form, she set the fastest times by a South African woman this year in the 100m (11.49 seconds), 200m (22.89) and 400m (51.52) events.
Thipe, trained by her husband, Eugene Thipe, who also coaches SA men's 100m record holder Simon Magakwe, is a three-time finalist at the African Athletics Championships.
Of the 10 local athletes to have tested positive this season, five are senior track and field competitors, two are juniors and three are road runners.
Evans said athletes were taking supplements and substances without understanding what they contained.
"During the IAAF World Junior Athletics Championship in Barcelona (in July), we had a discussion with the athletes," Evans said.
"We advised them not to use any substances.
"If they have to buy any medication, they should first get an expert opinion.
"The next moment, one of the junior athletes is off to a pharmacy to buy some nose spray.
"The pharmacist does not understand her and sells her something containing a banned substance. That is just stupid."
Among the athletes who have failed doping tests this season are Comrades Marathon winner Ludwick Mamabolo, who is facing a hearing after testing positive for methylhexaneamine, and former world junior long jump champion Luvo Manyonga, who tested positive for methamphetamine, commonly known as 'tik'.
