General Fernando Azevedo e Silva, head of the Olympic Delivery Authority (ODA) for Rio 2016, has quit his post just 18 months before the start of the Games.
Brazilian President Dilma Rousseff received his resignation this week and in a brief statement, praised Azevedo de Silva for his "dedication and efforts".
The army general had held the job since October 2013 and went to the Presidential office to hand in his resignation letter yesterday.
Edinho Silva, who was Rousseff's election campaign treasurer in 2014, is rumoured to be Azevedo e Silva's replacement although there has been no official announcement on who will take over the role.
Rousseff is thought to be keen on hiring Silva to strengthen dialogue within Brazil's sports sectors following the controversial appointment of George Hilton as Sports Minister in December.
The Brazilian President's decision to give Hilton, who is a member of the Brazilian Republican Party from Alagoinhas in the north-east of the country, the job was met with fierce criticism from Non-Governmental Organisation Athletes For Brazil as he has undertaken very few sport-related projects in his career.
A successful Sports Minister is seen as integral to staging a well-received Olympic and Paralympic Games and the organisation wrote a strongly worded statement in response to Hilton's appointment.
"We demand a lot more respect and attention to everything related to sports in Brazil, something that is far from happening considering the criteria, or the lack of, used to choose the new Minister," the statement read.
"Unfortunately, for years the Sports Ministry has been used for political bargaining."
The latest news will come as a blow to Rio's preparations ahead of the Games, which begin on August 5 and finish on August 21 next year, and follows the ODA's announcement last month that public and private spending for the Olympics had reached almost R$38 billion (£9 billion/$14 billion/€12 billion).
The ODA coordinate Olympic spending with national, state and local Governments and they have a strong involvement with the overall planning of the Games.
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