Last month 40 developing and industrialized countries agreed on two separate multi-billion dollar funds, managed by the World Bank and regional development banks, one to help developing countries cut their contribution to climate change and the other to help them prepare better for more storms and floods.
The developing world blames industrialized nations for climate change after decades of emitting planet-warming gases such as carbon dioxide from burning oil and coal.
The NGOs doubted the World Bank's qualifications to fund projects which curb carbon emissions given its history of loans to coal plants, including one this year to an Indian plant which will use the latest, cleanest boilers.
"Clean must mean 'clean', not 'slightly less dirty'," said a statement from the groups including Greenpeace, Friends of the Earth and ActionAid, on the fringes of a U.N. climate conference in Germany.
The Bank rejected that criticism, saying that such projects had "a largely beneficial impact on the environment by shifting production from small polluting installations to larger, cleaner, more efficient energy plants".
The U.N.-led Kyoto Protocol also supports such cleaner coal projects and U.N. climate chief Yvo de Boer repeated that support.
"I think given the pace at which coal-fired power plants are being built every delay means more sub-optimal plants."
"I think it's great," he said of the funds.
The NGOs also complained that some of the new funds would be in loans instead of grants, risking indebting poorer nations.
"It is highly inappropriate to issue loans for adaptation, given that rich countries are overwhelmingly responsible for climate change," their statement said.
De Boer agreed that the funds must not re-direct general overseas aid. "It's important not to re-label ODA (overseas development assistance) and turn it into loans," he said.
The World Bank said last month that "donor contributions to the Climate Investment Funds will be new and additional to existing aid commitments".
(Reporting by Gerard Wynn, Editing by Giles Elgood)