The organisations are concerned that accepting funds from a government waging war without full international consent could undermine their independence and credibility among donors and stakeholders.
"We have decided against approaching the Government for funding," said William Day, chief executive of CARE International UK, which runs water projects in central and southern Iraq. "There are significant risks to us and our ability to act effectively if we take money from a government perceived as belligerent."
Oxfam is taking a similar position, while Christian Aid says it is not applying for funds because it wouldn't be able to use them while fighting continued. CAFOD and ActionAid say they have no projects eligible for the funding.
Save the Children, in contrast, has decided it will take extra funds providing they come through the usual channels. "If there are strings attached or there was a public perception of that, we would reconsider," said Brendan Paddy, senior media officer for emergencies.
The question of accepting government funding in the build-up to war in Iraq has been under intense debate in the British Overseas Aid Group.
"It hasn't been acrimonious, but there has been a lot of soul-searching," said Beverley Jones, head of the international division at CAFOD.
All the aid charities say they will reassess the position once fighting stops, when their main concern will be operating independently of the US and UK armed forces.
General Tommy Franks, commander of the US forces, has made it clear he intends humanitarian and reconstruction work in Iraq to be directed by the armed forces and to last 18 months or more.
"We face a complex set of variables which make it hard to plan," said Day. "But the notion of packing cases labelled CARE International being unloaded from the back of an RAF Hercules does send out some wobbly signals."
Roger Riddell, international director of Christian Aid, said human need might override concerns about independence. "If people in a village needed food, and the only transport was the military, my answer would be to work with the military."
Short announced last week that an extra £10 million is being allocated to humanitarian work in Iraq, mostly through United Nations' agencies which are expected to lead the relief effort.
Aid charities point out that this is not new money, but comes from the Department for International Development's contingency fund. They contrast the figure with the £1.75 billion allocated by the Treasury to the Ministry of Defence for operations in Iraq.