A spokesperson for Tube Lines, a consortium that includes Bechtel, Jarvis and Amey, said TFL's EC claim was identical to the High Court case. The commission is investigating the compatibility of the public-private partnership with European Union state aid rules. It is due to make a decision next month.
The Tube Lines spokesperson said: "We think TFL should withdraw its complaint. It would be the best outcome of all."
The consortium, which will modernise the Jubilee, Northern and Piccadilly lines, said the TFL court action had delayed the scheme by a year. Tube Lines plans to spend £4.4bn on improvements in the next seven-and-a-half years.
Tube Lines chief executive Terry Morgan added: "After two failed court cases and four years of debate and argument, enough is enough. Tube passengers will feel they have waited too long for the improvement programmes to commence. All sides should now work together so the investment can begin."
Transport for London, which is headed by Bob Kiley, is believed to have spent £4m on legal fees opposing the PPP.