However, it did not address the lack of spending or explain why more funds had not been used.
Asked about the audit on Thursday, Brazilian Sports Minister Aldo Rebelo said the federal government was not responsible for delivering the games. He said that fell to the city and state of Rio de Janeiro.
He added "the works are on time, and there is no delay."
However, the International Olympic Committee has also expressed concern about the preparations recently, with some members comparing it to those for the 2004 Athens Olympics.
Earlier this month, Carlos Nuzman, the president of the Brazilian Olympic Committee, was grilled in Buenos Aires by IOC members concerned about repeated delays.
IOC inspectors also visited Rio earlier this month and urged organizers to speed up, saying more cooperation was needed among local, state and national officials.
In a recent interview with The Associated Press, Leo Gryner, chief operating officer of the organizing committee, acknowledged games preparations got off to a late start. He said the delay amounted to "six to eight months," though the auditor's report suggests a more substantial delay.
The organizing committee has yet to announce its operating budget, which is expected to be between $3.5-4 billion. That is the budget to run the games themselves. A separate capital budget and mix of public and private money, and also not yet announced was estimated at $11.6 billion in the original bid. Gryner said it was expected to grow by at least 35 percent.
Gryner has acknowledged that $700 million in public money may be needed to balance the operating budget, due partly to a shortfall in the sale of sponsorships.
The TCU report pointed out that delays could run up costs on construction projects.
"Such lack of planning makes it difficult for potential national suppliers to prepare for the increase in demand, which opens the possibility for delays, international contracting, emergency contracting, etc.," the report said.
The report also raised issues surrounding the construction of a canoe-slalom venue in a poor area of northern Rio known as Deodoro. Canoe federation officials have expressed concerns the venue might be moved out of Rio.
The costs of staging mega-events like the Olympics, and next year's World Cup, were partly behind large streets protests in June during the Confederations Cup, and warm-up tournament for the World Cup.
Millions of protesters took to the streets, angry that Brazil is spending billions on sports events in a country with poor public services, soaring taxes and stark social inequality.
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Follow Stephen Wade at http://twitter.com/StephenWadeAP