It claimed that the "seriously flawed" plan would lead to transport chaos outside London.
SERA claimed that much more needed to be done to improve transport links between locations in the South East outside London and the Olympic Park.
It is particularly concerned about plans to provide access to the Olympic Rowing lake at Eton Dorney, near Windsor.
"Overall, we remain deeply concerned at what we believe is the overly London-centric focus of the transport plan," says a SERA document published this week.
"The failure to reflect the region's significance as a gateway to the UK and the base for so many visitors to the Games is a serious flaw in the structure of the plan."
SERA has put forward a list of recommendations that includes extending the proposed Olympic Javelin rail service, running along High Speed One between Ebbsfleet in Kent and Stratford. It claims that some Javelin services should start further south at Ashford.
The Olympic Delivery Authrority (ODA) should also make cash available for a new park and ride site at Windsor that could take people to the Olympic rowing lake at Eton Dorney, says the report.
Meanwhile, the plan to make Taplow rail station the main entry point for spectators for the rowing lake was deemed "inappropriate".
The ODA should instead focus on transporting passengers to the rowing lake from Windsor, Maidenhead and Reading, says the report.
It adds that more needs to be done to integrate ticketing with public transport services in London and those in the South East.
An ODA spokesman said: "We welcome their views and the plan will be continually reviewed right up until the games.
"Schemes such as the Thameslink programme and the delivery of the new high speed trains in Kent will help enhance links in the south east to the Olympic Park in Stratford."