The delays caused two AP reporters and scores of other travellers to take at least 50 minutes to make the 6- to 7-minute ride out to the Olympic Stadium. Other riders complained on the social networking site Twitter about delays up to 2 hours, and barricades were put up to control the crowds at the train station.
Hours later, officials acknowledged that delays up to an hour were continuing Tuesday night, blaming signal problems.
Three days before the Olympics officially begin, London's extensive subway and train system is facing a major test with officials expecting up to 3 million more journeys a day during the games.
A spokeswoman for Southeastern, the company that operates the route, said there were problems outside London and further down the track that affected the new high-speed "Javelin" train. The train left nearly an hour after its departure time.
London transport officials already conceded earlier Tuesday that Olympic fans and millions of working Londoners — including Prime Minister David Cameron — will bustle and battle to get about.
"It will get busy," the city's transport chief, Peter Hendy, told reporters at the main Olympic press centre. "It has got busy already. There will be some queues."
The "Javelin" service aims to move around 25,000 people an hour at peak times to the Olympic Park at Stratford in the east of the city. The service is set to run 24 hours a day and has planned 200 extra trains every day during the Olympics, offering a total of 6.2 million extra seats.
The delays Tuesday followed other problems on Monday night when two other train links serving the Olympic Park — one subway line for central London and another for an overland train — temporarily went down as thousands of volunteers rehearsed for Friday's opening ceremony.
"We got everybody home. It was a successful dress rehearsal and we're looking forward to delivering the real thing on Friday," Britain's Transport Secretary, Justine Greening, said Tuesday. "But, of course ... on a transport system as complex as London's, things do go wrong."
"Even though one line is down, the rest were working. That shows part of the resilience that we've got," Greening said.
Parts of the London underground system trace back to the 1860s. The system averaged about 12 million rides a day before the Olympics, and that is expected to rise to 15 million journeys a day during the games.
Cameron has said he's going to use public transport for some trips during the games and not the VIP Olympic road traffic lanes that open Wednesday.
Britain spent over 6.5 billion pounds ($10 billion) since winning the bid on upgrading London's sprawling transit system. But public transport will face challenges with venues spread across London.
Tennis will be at Wimbledon in the leafy suburbs of the southwest, while beach volleyball takes place in the heart of the city, close to Cameron's Downing Street residence.
The weather can also be a problem. Another train station in east London was out of service temporarily Monday because of high temperatures that affected overhead power lines.
"It's part of the challenge," Greening said.
While trying to provide a seamless transport service for the 18,000 athletes, 11,000 officials, 26,000 media and over a million tourists at the games, London also has to remember its own busy residents.
Officials hope the Olympics "don't disrupt Londoners more than we have to," Hendy said, but some locals may feel like second-class citizens.
Dedicated Olympic traffic lanes that take effect at 6 a.m. Wednesday already have left some Londoners unhappy. Drivers of the city's famous black cabs demonstrated Monday over the fact that they can't use the special Olympic lanes.
But it's not all bad news. Travel is free for ticket-holders to their Olympic events.
Wireless Internet is also now available inside some London subway stations for the first time. If you're stuck in those spots, at least you could keep track of the travel chaos online.
Associated Press Writer Danica Kirka contributed to this story.
Follow Gerald Imray at http://twitter.com/GeraldImrayAP