Rio de Janeiro Mayor Eduardo Paes said the iconic Guanabara Bay won't be clean in time for the 2016 Olympic sailing competition, breaking a promise made when the city won the hosting rights in 2009.
"I am sorry that we didn't use the games to get Guanabara Bay completely clean, but that wasn't for the Olympic Games - that was for us," Paes said.
"That was something that we could not accomplish that was in the bid book."
Paes said the sailing competition would be held in unpolluted waters, either outside the bay or at its entrance.
He added that athletes' health would not be at risk from debris and sewage that drains into the bay, which skirts the city.
The bay can often be seen in photographs of the tourist landmark Sugarloaf mountain.
Brazil is facing increased scrutiny before the World Cup opener on Thursday after delivery of almost all 12 new or refurbished soccer stadiums was delayed and over budget.
Paes' comments come five weeks after John Coates, an International Olympic Committee (IOC) vice-president, said Rio's Olympic preparations were the "worst ever". Paes said the clean-up of the bay was one of few shortcomings in preparations.
The city has focused on legacy projects including a new metro line, bus rapid-transit lines that extend longer than Rio promised the IOC, and a handball stadium that will be converted into a public school.
The Olympic Stadium is ready, Olympic Park construction is on schedule and private funding accounts for about 60 per cent of the total budget.
World Cup delays and cost overruns have reinforced international mistrust of Brazil's ability to deliver, and Rio is hoping to correct that perception, said Paes.
The Olympic budget of 36.7 billion reais (HK$126.3 billion) could rise by as much as 20 per cent, he said.
"We really do believe that we are on time, and that we are going to deliver great games," Paes said. "Lots of public money is being saved to build the Olympic values and the legacy we want to deliver. We're not going to leave any white elephants."
He said Rio could leave a legacy comparable to the 1992 Barcelona Games, which are viewed as the best at improving urban development.
Additional reporting by Associated Press