The charity, which receives 80 per cent of its funding from the government, has criticised plans to devolve the commissioning of services for witnesses and victims of crime to 42 new locally elected police and crime commissioners.
The charity said the new local commissioning system would cost £21m to set up and lead to inconsistent service provision around the country.
Victim Support receives £38m a year from the Ministry of Justice to provide a national helpline for crime victims, a community service to support victims of crime and support for them in every criminal court. Other charities are also funded to provide specialist services such as counselling.
Javed Khan, chief executive of Victim Support, told Third Sector: "Eighty per cent of our funding comes from central government, so it is a very bold step we have taken. It is not something we have done before, but we have done it for very good reasons."
He said he did not think the government would penalise Victim Support - by putting its services out to tender, for example - for criticising a key policy.
"I could say to my staff ‘we are the front runner because we are already on the ground doing the work’ and ‘we could put in 42 bids and win most of them’ – but that is not the point. The point is that we fundamentally believe this is wrong. And I think government will respond to that position rather than hold it against us, because we have done it from a principled position."
He added: "This is not about having a battle with the Ministry of Justice; it is about giving honest advice from those doing the work for many years. We believe their intentions are good."
Khan said the organisation was not opposing the new system simply because it received a large contract under the current one and did not want that to change.
A spokeswoman for the Ministry of Justice said: "We currently spend £66m a year supporting victims and witnesses of crime, and our proposals will raise up to £50m extra. This will increase, not reduce, the support and help on offer.
"Police and crime commissioners will put the needs of victims of crime at the centre of their agenda and will be required by law to consult victims in setting policing priorities in their local areas."