Pistorius, who wears carbon fibre blades and was cleared to compete against able-bodied athletes by the Court of Arbitration for Sport in 2008, was named in South Africa's relay team last week.
South African media reported that the IAAF would not allow Pistorius to run in anything but the first leg due to concerns over the safety of other athletes because of his prosthetics and the rough and tumble nature of relay changeovers.
An IAAF spokesman said the position had not changed since the world championships in Daegu last August.
"At the Daegu 2011 IAAF world championships the decision for Oscar Pistorius to run the opening leg of the 4X400 relay was taken by ASA (Athletics South Africa) and not by the IAAF," he said via email.
"Now it will be the same for the Olympic Games. The decision will be taken by Athletics South Africa. It was always like this."
This, however, seemed to contradict what IAAF head Lamine Diack said last year.
"This person is a particular case," Diack said at the Daegu championships.
"The only thing we said to the South African federation is that if he wants to run in the relay, he must run the first leg to avoid danger to other athletes."
South Africa's Olympic chief Gideon Sam said on Wednesday that they will not seek an IAAF ruling over the matter.
Sam, president of the South African Sports Confederation and Olympic Committee, said it was up to the relay team and coaching staff to decide where Pistorius runs.
"“We won't give in to any outside interference over where Oscar is allowed to run, that would amount to discrimination," Sam said.
"The debate over whether he gets an advantage from his blades is over and, like any relay team, be it athletics or swimming, it is now up to the team to decide where he runs."
Pistorius failed to meet SASCOC's stringent qualification criteria for the 400m, but will still take part in the individual event because he is a member of the relay team.
Although he did not run in the final, he was part of the 4x400m team that won silver in Daegu and is South Africa's fastest runner over that distance this year.
“"Oscar ran a qualifying time in South Africa and has worked very hard in running all over the world, so there's no reason not to include him," Sam added.
South Africa's deputy minister of sport, Gert Oosthuizen, said the government backed the 25-year-old athlete's selection.
"As part of our drive to normalise society, we want to mainstream disabled people, that is the declared policy of government," Oosthuizen told Reuters.
"We always want them to be able to showcase what they can do and to destigmatise them."
Sam also announced that SASCOC would pay incentives to all South Africa's medal winners at the Olympics.
Gold medalists will receive 400,000 rand (£31,220), silver 200,000 rand and bronze 80,000 rand.