Rio Mayor Eduardo Paes waved the flag after stepping off the plane with other officials and Brazilian athletes who competed in London.
The flag was handed to Eduardo Paes on Sunday in London before the flame at the Olympic Stadium was extinguished.
The move marks the official start of Rio’s preparations for the 2016 Games.
Arriving on Monday with the flag, Eduardo Paes was accompanied by Carlos Arthur Nuzman, president of the 2016 Games Organising Committee, Rio Governor Sergio Cabral, and the country’s team of athletes.
Brazil finished 22nd in London 2012, winning 17 medals, two more than its previous best in Beijing.
Rio de Janeiro will be the first South American city to host the Olympics. The city has yet to construct the Olympic Park and other venues, and many have expressed concern about how much work there is to do ahead of the event.
During a visit in June, members of the International Olympic Committee (IOC) said that timelines were “already very tight” and that “the amount of work to be completed is considerable”.
Worries about Olympic readiness are not new, but that not since Athens have there been so many questions about a host’s ability to stage the Olympics.
The transport system in Rio already struggles to serve its six million people.
But Eduardo Paes has promised to transform the city’s infrastructure, and the government says all of the Olympic venues will be finished a year before the games start.
They will be helped by the fact that they have something of a dress rehearsal, when the World Cup arrives in Brazil in 2014.
As the delegation touched down, a group of demonstrators were gathered outside the airport in Rio to protest against planned evictions connected to the Olympics planning, according to the Associated Press.
The London Olympics were brought to a close on Sunday night with a spectacular musical ceremony, featuring some of the biggest names of British pop, including the Spice Girls, George Michael and Elbow.
In a separate development on Monday, a female athlete from Belarus was stripped of her gold medal in the London Olympics after failing two drugs tests.
The shot putter, Nadzeya Ostapchuk, was the first athlete to lose a medal in the 2012 Games due to doping.
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