Pistorius was the leadoff runner in the semifinals at the world championships in Daegu last year after the IAAF had raised concerns that that his carbon fiber blades would endanger others in the race. South Africa won silver but Pistorius did not run the final.
Pistorius is the first amputee runner on blades competing in the Olympics and his four-year battle to overturn a ban and qualify to compete in track's premier event became one of the most compelling stories of the games.
Pistorius is set to run in the individual 400 on Saturday and is expected to run the relay next week.
IAAF President Lamine Diack said Tuesday that it was fully up to the South African federation to decide on the makeup of the relay, raising the possibility that Pistorius will be running in the bunch once athletes leave their lanes after 500 metres.
Diack said that if South Africa wants to let him run a different leg "it can do so, it is no problem for us."
So far he has run several races this season in relay legs other than the first, causing no problems. However, the IAAF is sticking to its advice that "common sense" shows it would be safer to have Pistorius run in lanes.
"It is better he run the first leg because in the first leg you are in lanes," Diack said.
Pistorius was angered last year when the South African federation made him lead off in the wake of the IAAF concern, since he is known as a slow starter. He would benefit from a running relay exchange later in the race.
Since Daegu, he said he was bent on running different parts of relays to show he is not a danger to other runners.
Diack conceded there was little the IAAF could do, especially since Pistorius ran the third leg at the African championships in Benin early this summer.
"That championship is only a step lower that a global championship," he said.