Chuene first denied knowing that tests were carried out on the runner in South Africa before her 800m world title win but later admitted he had known.
He then expressed outrage when governing body the IAAF ordered its own tests after the Berlin championships.
But the Athletics South Africa council has backed the under-fire Chuene.
After meeting for several hours on Thursday, they released a brief statement saying it "unanimously expressed confidence in the current ASA leadership."
Chuene refused to comment after the meeting but South Africa's opposition Democratic Alliance party said the statement was "exceptionally disappointing."
"The need for Chuene to go is a no-brainer - so it is of deep concern that ASA appears to have given him a vote of confidence," they said.
The mere fact that SA athletics thought they could get away with this shows how far removed they are from the real world
"Chuene lied to the nation. He embarrassed South Africa internationally. And he breached Caster Semenya's right to dignity. What more does someone need to do to face disciplinary sanctions?"
However, the South African Sports Confederation and Olympic Committee is conducting its own investigation into the Semenya case.
Chuene admitted on Saturday that he had lied to the South African public about his knowledge of the tests, conducted on Semenya in Pretoria on 7 August, but said the deception had been intended to protect Semenya's confidentiality.
He said that he had lied about the matter to protect the teenager's privacy.
The International Association of Athletics Federations (IAAF) began a gender verification process ahead of the race in Berlin and, pending the outcome, allowed Semenya to participate in the 800m final.
Semenya first burst on to the world stage in July when she ran one minute, 56.72 seconds for the 800m in Bambous, smashing her previous personal best by more than seven seconds.
Though South African officials insisted no gender tests were carried out within the country, it has emerged that the IAAF asked for Semenya to be withdrawn from the South African team for the World Championships following initial tests conducted locally, before the event.
However, Athletics South Africa insisted she should run and has since said it is certain she is female, a claim backed up by her family.
Semenya won the world title in another personal best of 1:55.45, two seconds clear of defending champion Janeth Jepkosgei.
The IAAF ordered more tests following that victory, with the results due in November but BBC Sport understands they are likely to show Semenya has an intersex status, exhibiting both male and female sex characteristics.