Save the Children, Christian Aid and War on Want have argued that the $4bn (£2.1bn) that will be raised by the sale of bonds by the International Finance Facility for Immunisation's six member countries could have been raised in other ways.
"Ultimately, if the money is spent well and goes towards the children who need it, then that would have a fantastic effect," said Sarah Hague, economic adviser at Save the Children UK. "But it is not new money, and they are just going to have to cut aid to repay the bond.
"The countries that have launched the bond could have come up with $4bn, without having to borrow it. That is a small amount compared with what they should be giving in aid anyway."
Anna Thomas, policy manager on development finance at Christian Aid, said: "The Chancellor has pledged that 0.7 per cent of national wealth will be spent on international aid, so the repayment of this loan must be on top of that."
Thomas added that, in addition to raising its own money for aid, the Government should also be helping developing countries to harness their own wealth.
"There is a lot of leakage from developing countries because money is moved overseas, usually to avoid taxation," Thomas said.
John Hilary, campaigns and policy director at War on Want, said there were many ways in which Gordon Brown could raise funds without in the long run cutting the levels of aid the UK gives to the developing world.
"A stamp duty of 0.005 per cent on sterling currency transactions, for example, would raise 10 times the amount that the IFFIm is set to raise, and would not be restricted in terms of its time span," Hilary said. "Yet the Chancellor has rejected it, and I think he needs to explain why."
However, Pesh Framjee, head of charities at accountancy firm Deloitte & Touche (the auditor for IFFIm), expressed a different view.
"Charities are always looking for new ways to set up funding relationships - and this bond is a new way of doing that," he said. "The bond is also a good way of attracting a range of people who wouldn't otherwise have engaged in development giving."