The removal of Connex's rail franchise in the South East is to be investigated by the National Audit Office.
The appointment of South Eastern Trains is being investigated
The Strategic Rail Authority (SRA) stripped the French group Connex of the franchise in June 2003, giving poor financial management as the reason.
Regional trains have been operated by government-run South Eastern Trains, a subsidiary of the SRA, since then.
The appointment of South Eastern Trains, and the government subsidies it receives, are also being investigated.
A new franchise holder for the South East is expected to take over in 2005.
The new franchise holder is also set to run high speed services on the new Channel Tunnel Rail Link from 2008 or 2009.
Some unions have said that they want to keep South Eastern Trains under public control, arguing reliability has improved.
The South East franchise covers routes between Kent and East Sussex, and London.
The National Audit Office has confirmed that an inquiry will look at the ending of Connex's contract and the selection of its successor, with a report to parliament expected in the summer.