Louise Ellman, chairwoman of the House of Commons Transport Committee, in a letter to Patrick McLoughlin asks him about the terms of reference for the so-called "independent review".
She writes: "There have been press reports that three Department for Transport staff have been suspended as a result of the cancellation of the West Coast Main Line franchise competition. Could you confirm this, say at what grade the suspended staff are employed, confirm their tasks and role with respect to the West Coast Main Line franchise and confirm what reporting arrangements operated between them and the relevant ministers?"
She adds: "Could you let us know whether the problems raised with the West Coast Main Line franchise and subsequent suspension of staff are likely to have ramifications for other aspects of your department's work, particularly conclusion of the Thameslink rolling stock procurement."
Mr McLoughlin, who will appear before the committee on October 31, has laid the blame for the problems with the Scotland-to-London franchise bid "fairly and squarely" with DfT.
Yesterday, the Prime Minister admitted he had been surprised when Aberdeen-based FirstGroup won the franchise over Sir Richard Branson's Virgin Rail, which has run it since 1997.
"I had a series of letters and other things from Branson, which I wanted to study very carefully and I asked the Cabinet Secretary, personally, to look into this decision carefully to make sure that everything was right," he said.
Mr McLoughlin must decide if Virgin should run the line after December 9 when FirstGroup should have taken over or to have DfT run it as is the case with the other main Scotland-to-London line on the east coast.