The rejection came in the joint HM Treasury and Home Office response to their consultation on the Government's proposed measures, published in May, to protect charities from terrorist abuse.
Some of the 23 respondents to the consultation expressed concern that humanitarian work in certain parts of the world would be virtually criminalised unless trustees who had taken all reasonable steps to avoid abuse of their funds by terrorists were protected from the risk of prosecution.
In its report on the consultation, Review of Safeguards to Protect the Charitable Sector (England and Wales) from Terrorist Abuse, the Government dismisses such a defence as neither necessary nor justifiable.
"The breadth of the UK terrorism legislation, with respect to terrorist financing, reflects the importance of denying terrorists financial support," it says. "The legislation is in place to enable law enforcement to tackle abuse and negligence where it exists and where charities or individuals have acted intentionally or irresponsibly.
"Financial infrastructure is required to sustain international terrorist networks and promote their goals. The charitable sector cannot and should not be complicit, incidentally or otherwise, in supporting such ideology and networks."
The report acknowledges sector concerns about the independence and reputation of the Charity Commission in the light of the Government's call for it to work closely with counter-terrorist agencies. Many respondents felt that it could lose the goodwill of the sector.
But it says: "The Government is of the firm view that the Charity Commission is uniquely placed to deal with abuse where it does occur in charities". It welcomes the regulator's commitment to redirect a "significant level of existing resources" to counter-terrorism work.
The Government also repeats its call for the commission to become more proactive in investigating perceived threats, including, "where appropriate", site visits to charities.
It says the regulator should act proportionately to the risk to avoid imposing unnecessary burdens on the sector. It also acknowledges respondents' concerns about a "one size fits all policy", and says the commission should produce practical advice for trustees on assessing risk to their own organisations.
It also says it will work with the commission to produce guidance for humanitarian charities worried about being designated as supporters of terrorism by foreign governments - especially that of the US.
"Advice should reflect the differing stances taken by members of the international community to certain organisations and the risks and consequences associated with working abroad and under foreign jurisdictions," the report says.
It says the Government acknowledges the sector's view terrorist abuse of charities is very low, but describes the risk as significant: "Such exploitation is unacceptable, and the impact of even one proven case involving a charity is potentially significant for public trust and confidence in charity."