Desalination is the wrong way to handle water shortages around the world and could exacerbate climate change.
But independent scientists disputed the findings and said desalination plays a minor role in global warming.
The World Wide Fund for Nature said its study found that desalination uses large amounts of energy, emits greenhouse gasses and destroys marine life in some coastal areas.
"The rate of building these desalination plants seems to be growing exponentially," said Jamie Pittock, who heads WWF's freshwater program. "If that continues ... greenhouse gas emissions would accelerate and increase climate change dramatically," he told The Associated Press.
WWF estimates that there are about 1,000 desalination plants around the world, Pittock said, adding that it was difficult to obtain good data and that more research was needed.
Desalination has become a growing trend particularly in Australia, the Middle East, Spain, the United Kingdom, the United States, India and China, the report said.
The Persian Gulf meets an estimated 60 percent of its drinking water needs through desalination. Perth in Australia is looking to cover one-third of its freshwater demand using desalination.
In Spain, 22 percent of the desalinated water is used for agriculture, according to the document.
Making more drinking water with the help of desalination plants "creates a wasteful attitude to water use," said Pittock, adding that in most cities vast amounts of water are wasted.
People should set up more water-effective technologies in houses and businesses, reduce the leakage in pipes and recycle waste water, he said. "In most cities desalination plants are not required."
Marine life is put at risk by desalination plants, the report said. As the seawater is taken in, small life forms such as plankton, eggs and fish larvae are also removed.
The brine the highly concentrated saline water discharged from the plants is mostly sent back into the sea where it increases the salinity of the water, posing a threat to sea life and disrupting the ecosystem.
In the United States, some states such as California and Florida, that are short of water, plan large desalination plants in enclosed sea areas, Pittock said. The saline discharge from plants in enclosed areas such as Monterey Bay in California can destroy sea grass and kill fish, he added.
Seawater desalination should be limited to places where no better solution can be found, the report said.
"There needs to be a thorough assessment whether these plants are really needed," Pittock said.
But experts outside WWF said the technology could be used with less environmental impact.
Ger Bergkamp, who heads the water program at The World Conservation Union known under its acronym IUCN said the problem with desalination plants is much more the negative impact on the ecosystem than greenhouse gas emissions.
"The number of desalination plants that exist is so small that their contribution in emissions is at this point in time still minute," Bergkamp told the Associated Press.
Instead of opposing a technology that could help many countries out of their water crisis, it would be better to find ways how it can be improved, he said.
Desalination plants could be made more energy-efficient and powered by renewable energies, he added.
Looking into ways to discharge the brine far enough from the coast so that it can dilute or finding alternative uses for the saline discharge in other industrial processes might minimize the environmental impact, said Bergkamp.
Professor Daniel Favrat of the Industrial Energy Systems Laboratory with the Swiss Federal Institute of Technology in Lausanne denied that desalination of sea water poses a major problem for global warming.
"There are a lot of ways to do desalination which are relatively climate-neutral," he said.
Not all the techniques used today are harmless for the climate but in theory desalination can be done without aggravating climate change, he told the AP.
The plants can be placed next to power stations so that they can run on the heat released as a byproduct of electricity generation and avoid additional greenhouse gas emissions.
"In Saudi Arabia there are power plants which produce energy and do desalination at the same time," he added.