Five flights between Sao Paulo and the US were turned back after a radar in north Brazil shut down for two hours.
The problem occurred just one day after Brazil's president said air safety in the country met international norms.
The radar, at Manaus in Amazon state, covers a major point of entry into the country, including many routes between Brazil, the US and Central America.
Meanwhile, the flight recorder from the Tam Airlines plane that crashed in Sao Paulo on 17 July has been recovered.
Brazilian officials said they had located the real flight recorder after first mistakenly sending a piece of the plane's fuselage to the US for analysis.
Nearly 200 people died on Tuesday when the jet left the runway at Sao Paulo's domestic airport, crashing into a building.
Twin challenges
According to Infraero, the company that runs Brazil's airports, the radar at Manaus shut down for just over two hours.
After the radar was fixed, it took another two hours before it was fully functioning.
The flights that were affected were travelling in both directions between the US and Brazil.
Two American Airlines planes reportedly had to make unscheduled stops in Manaus.
The exact cause of the problem is not clear, but flights have been returning to normal.
In a speech to the Brazilian people on TV on Friday night, President Luiz Inacio Lula da Silva acknowledged that the air traffic system in the country was experiencing difficulties but said it was compatible with all international standards.
In normal times the fault with the radar might almost have passed unnoticed outside the country, says the BBC's Gary Duffy, in Sao Paulo.
But after two major air accidents in a year, one of them over the Amazon, every problem is now attracting international attention, he adds.
The government is facing the twin challenges of maintaining international confidence in Brazil's air traffic system while also dealing with widespread anger within the country over its handling of the issue.
^ Back to top | BBC Sport Home | BBC Homepage | Contact us | Help | ©