Lane closures on the A3, A12, A13 and A40 were planned to prepare the roads for the Olympic Route Network (ORN), Transport for London (TfL) said.
By midday the traffic situation on the A12, A13 and A40 - which saw the worst delays - had improved, the BBC reported.
The ORN in London will become active across London on July 25, two days before the opening ceremony of Olympics.
Garrett Emmerson, TfL's chief operating officer in charge of streets, said he "sympathised" with the motorists who were stuck on the roads for long hours.
But he added that TfL has been warning people to avoid driving into the capital from mid-July because driving on certain roads "is going to become very difficult".
One motorist using the A13 said his normal hour-long drive from Swanley to Redbridge was expected to take about two and a half hours.
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Earlier in the day there was also heavy traffic on local roads in Canning Town and West Ham in east London.
Congestion was also seen in central London, with delays in Whitehall, Shaftesbury Avenue and Trafalgar Square.
Authorities have warned that there will be additional road closures across London as the Olympic Torch continues its procession, with Croydon, Sutton, Merton and Wandsworth to be visited.
Dozens of motorists vented frustration at the delays on Twitter.
Chris Rowe tweeted: "Traffic on A12 and A13 unbelievable this morning."
Looking ahead to the full Olympic Route Network coming into force on Wednesday, Richard Cowley wrote: "Think this is rough - wait for the 25th."