Services on a key transport route to the Olympic Park were suspended for several hours after a fire alert.
The problem meant no trains were running on a section of the Tube's Central line which serves the Olympic Park station of Stratford. To add to Olympic travellers' difficulties, rail services in and out of Liverpool Street main line station were affected by a signalling problem.
The Central line was suspended between Liverpool Street and Woodford/Newbury in both directions but was reopened by around 10am.
A Transport for London (TfL) spokesman said: "The suspension is due to a train being taken out of service at Leyton after the driver reported smelling smoke. This has been investigated and all passengers left the train and station without reported problems."
TfL had advised Olympic spectators to use other Tube and main line services to reach Stratford, including the Underground's Jubilee line, the London Overground and the Docklands Light Railway.
The main line difficulties at Liverpool Street were caused by an overhead wire problem between Elsenham and Stansted Mountfitchet in Essex. This was affecting travellers on services run by the Greater Anglia and CrossCountry train companies.
The problems around Liverpool Street come on another busy day for public transport as the first weekday evening football match takes place at Wembley Stadium.
This is only one of a number of Olympic events taking place in the capital, with TfL advising that London is expected to be exceptionally busy throughout the day.
TfL said people were heeding advice to avoid London if possible.
It added that while Tube journeys were up 4% on Monday, road journeys in London were down by 20%.