Chancellor Gordon Brown did not make any announcement about the Crossrail project in his annual spending review on Monday.
Transport Commissioner Bob Kiley had hoped it would be part of the government's spending plans for the next three years.
A further £2bn is needed to complete the project, which will link east and west London.
The government has already pledged £2bn to the £10bn transport link.
Work has started on the rail link which will provide transport between Heathrow airport in the west and the Isle of Dogs in the east.
It will also include a twin-bore tunnel between Paddington and Liverpool Street in central London.