In an email, entitled "strictly confidential" but obtained by O Globo, Paes asked the IOC to consider extending the BRT [Rapid Bus Transport] system, which involves exclusive lanes for public transport, as a contingency plan.
“In recent weeks, I’ve been trying to figure out what is really happening in the construction of Line 4 subway," the Mayor's message read.
"Deadlines and schedules…I heard from some people that the project is a high level of risk.
"All I can say is that the information is not clear.
"The Municipal Secretary [of Transport] Rafael Picciani already prepared an alternative, and I think we need to start studying it now and submit it to the assessment of the IOC.”
Phillip Bovy, the IOC's chief consultant for transport, is expected to travel to the host city for meetings tomorrow.
The extension to Metro Linha 4 is among the most important legacy projects of the Games, intended to improve the commute for more than 300,000 people a day.
If it does not materialise, it would be a huge blow for the Games and for the city.
Barra, the location for the Athletes' Village and the main Olympic Park, is a 30 minute drive from Copacabana and the Rio Centro zone in good conditions.
But it is invariably a two-hour drive in rush-hour.
A Games-lane is already going to be introduced for accredited personnel, but this could add to the congestion and will not be accessable for spectators attending the first South American Olympics, due to open on August 5.
IOC President Thomas Bach did not directly address this issue when asked about the concerns here today.
He said they are in "close and contact" with organisers and have "great confidence" the Games will be a success.