The decision is likely to affect Jarvis and Balfour Beatty. Jarvis won a £350m signalling and telecommunications contract for Thameslink and Balfour Beatty was chosen as preferred bidder for the £200m electrification package.
The Thameslink decision will lead to fresh concerns over projects such as the £800m East London Line extension and CrossRail. Reports at the weekend suggested that the government would be shelving the East London Line.
Transport campaigners said the Strategic Rail Authority, the body that oversees major projects, was discontinuing all large rail schemes in favour of smaller ones because it had run out of funds.
Sources close to the £3.3bn CrossRail scheme, which will link east and west London, said there was no indication that the scheme would be dropped.
CrossRail is due to report to ministers next month.