Pole vault silver medallist Renaud Lavillenie was booed by the Rio crowd for a second time in 24 hours - with Olympics chief Thomas Bach calling his treatment "shocking".
The Frenchman, 29, was in tears as he was barracked on the podium on Tuesday.
On Monday, he was booed by the partisan home crowd before his final vault - losing out to home favourite Thiago Braz da Silva in a dramatic final.
Bach said the crowd's behaviour was "unacceptable at the Olympics".
Lavillenie held his head in his hands on the podium and was later consoled by Brazilian gold medallist Da Silva, IAAF president Lord Coe and former Olympic and world pole vault champion Sergey Bubka after the ceremony.
London 2012 champion Lavillenie told French television: "It's disgusting, there is a total lack of fair play and I want to stress that the Brazilian is not involved at all."
Da Silva claimed a shock gold with his second attempt at 6.03m to win Brazil's second gold of the Games.
But world record holder Lavillenie said the "nastiness" of the crowd had "really disturbed" him and compared his treatment to that of African-American athlete Jesse Owens in the Nazi-era Berlin Games of 1936.
He later apologised, saying he made the Owens comparison immediately after the competition when very upset.
Rio 2016 chief spokesman Mario Andrada said: "As citizens of Brazil and as sports fans, we don't think booing is the right attitude, even when you are in a one-to-one competition and a young Brazilian has the chance to beat the world champion.
"We plan to intensify our dialogue with Brazilian fans through social networks to make sure that we behave as fans in a proper and elegant manner, without losing the passion for sport."
Appeals for silence were made before each race at the Olympic stadium on Tuesday.
"Those tears were tears of disappointment in this crowd. They should be ashamed. I can't let that go - it's not what competition is about," former 400m world record holder Michael Johnson told BBC Sport.
"Support the person that you want to support, but you don't boo someone else simply because they're competing against the person you support. They started that during the competition, it wasn't proper etiquette.
"It's really a shame and I think that he was really hurt. To then boo on the medal stand having not learned the lesson to begin with...some don't know better, but some I talked to were saying 'that's not what you do'."