The Office for Civil Society awarded the umbrella body a three-year contract worth £1.6m in 2009 to run the free site, which lists government funding opportunities available to third sector organisations.
The contract still has 18 months to run, but in its Modernising Commissioning green paper published this week the OCS said it would launch a new free site called Contracts Finder in March 2011.
According to the green paper, Contracts Finder will host "all central government tender documents and contracts".
The green paper said the government would "consider the relationship between Contracts Finder and Funding Central", which could provide similar services.
Ben Kernighan, deputy chief executive of the NCVO, said: "We will continue to provide the service for the remaining part of the contract and work with the government to ensure that any new services are complimentary and not duplicatory."
The OCS declined to comment on the matter.