The federation, established in 1996 as an umbrella body to represent the local independent rape-crisis centres in England and Wales, relied on a Home Office grant, which was awarded in April 2001 for a three-year period.
Ministers were meant to decide this April whether to renew the grant, but funding was suspended last summer.
In a statement made before the organisation closed at the end of 2003, the federation said: "It is remarkable timing that just as the Sexual Offences Bill is due to be enacted and just as the Government is due to report to the United Nations on action to eliminate discrimination against women, the Home Office chose to withdraw their financial support."
The closure has jeopardised the creation of a national database monitoring the experiences of rape victims, and also leaves local crisis centres without training services or a unified voice.
But the Home Office has defended its decision, saying that it froze funding because the federation was embroiled in an employment dispute with former members of staff, resulting in an out-of-court settlement.
"Home Office Ministers, having taken advice, decided that it was not appropriate for the Home Office grant to the federation to be used to fund either the settlement or the federation's associated legal costs," said a Home Office spokesman.
"We made it clear that we would be willing to resume payment of the grant once these problems had been resolved, and that we were keen to support the federation in its work."
The Home Office insisted that the funding cut would not affect local rape-crisis centres or the services available to rape victims.
However, campaigning group Truth About Rape, which worked with the federation, disputes this version of events.
"The last payment made to the federation was in the summer, a good eight weeks or more before any agreement was reached between former workers and the federation," said Helen Jones, spokeswoman for Truth About Rape. "So the decision to stop the funding seemed to be made before the point that the Home Office is referring to."
She added: "A project worker from the federation made an application to the Home Office for continued funding in order to secure a specific project in November, but as yet she hasn't even received a reply."