A loan from development financial institution FDN has made the start of construction works possible.
Both the city mayor and the director of the Metrobús BRT system have defended the project's construction.
The 11 loans pending congressional approval would serve to finance construction of rural roads, hospitals and waterworks, among other projects.
It is the biggest roadworks project in Brazil and the largest highway initiative being financed by the IDB.
The suspension was made at the request of local engineering company OAS.
Carlos Villalta had served in the position since January 2016.
The country's anti-corruption office is looking to join several corruption-related lawsuits against Brazilian construction giant Odebrecht.
The federal government's plan involves closing down national airport authority Infraero and privatizing some 54 airports all over the country, collecting an estimated 43bn reais (US$13bn) in canon payments, infrastructure investments and savings on spending.