In a report published today, the umbrella body warns: "The Government's heavy-handed approach could drive voluntary groups underground. It should be working to engage charities rather than alienating them."
The report pre-empts a joint Home Office and Treasury review on terrorist financing by UK charities, which is due to be completed in early February.
Lord Plant of Highfield led the 17-strong advisory group responsible for producing the document.
It argues that the Government has a "scattergun approach" to the issue: "Recent unhelpful statements from politicians have singled out charities as vehicles for financing terrorism without providing any evidence and without understanding the reality of charities' work."
The report refers to a lecture by Gordon Brown last October in which he claimed "many charities are at risk of terrorist abuse".
NCVO chief executive Stuart Etherington said: "No evidence has been put forward by the Government that the existing regulatory structure is not adequate to deal with the problem.
"The burden of proof is on the Government. What is the scale of the problem? What are the inadequacies with the existing regulations?"
The debate about charities and terrorist groups intensified last August when a BBC documentary alleged that Palestinian relief charity Interpal was funding groups associated with the militant body Hamas.
The Charity Commission, which is opening a third inquiry into Interpal, has begun 20 investigations into connections between UK charities and terrorist organisations since May 1998.
A Home Office spokeswoman said it was important that "any possible avenues for exploitation by terrorists" were closed off.
She said: "We want to work with the charitable sector to maintain high levels of public trust and confidence and to ensure that terrorists are not allowed to take advantage of charities."
A Cabinet Office spokesman said: "The Government will shortly announce the details of a consultation on this issue."