"Desalinating the sea is an expensive, energy intensive and greenhouse gas emitting way to get water. It may have a place in the world's future freshwater supplies but regions still have cheaper, better and complementary ways to supply water that are less risky to the environment," said Jamie Pittock, director of WWF's global freshwater programme.
According to Pittock, since a growth in the energy intensive technology would increase emissions and damage coastal and river habitats, greater emphasis on managing existing supplies should be given before the go-ahead is given to major water projects.
New desalination plants, which are primarily located in coastal areas, should also be subject to tighter impact assessments to minimise damage to the marine environment, he said.
Desalination plants already play a major role in providing water for drinking and irrigation in areas such as the Middle East, where freshwater supplies are scarce. But many other nations, including the US, China and Spain are turning to the technology to meet growing demands.
"Water supply, on a global basis, is a problem," said Richard Bowen, a fellow of the Royal Academy of Engineering. "Desalination is set to become more important because the demand for water is going to increase, and a large percentage of the world's population is situated in coastal areas," the BBC quoted him as saying.
The study was published as Australia announced plans to build one of the world's biggest desalination plants to supply drinking water to Melbourne.
Southern Australia has been in the grips of a six-year drought, the worst on record. The project, which is expected to be completed by 2011, is part of a scheme to "drought-proof" water supplies to the nation's second largest city.
According to the study's authors, advances in technology should attempt at developing alternative "manufactured water" systems, such as treating waste water.
"The basic problem is that by taking sea water and producing fresh water, you are going to get a stream of fresh water, which is what you want, but you also produce a concentrated salt stream. You have to be very careful what you do with that concentrated stream and where you put it back into the environment," said Prof. Bowen, from the University of Wales' School of Engineering, Swansea.
"There have been quite careful studies into the effects of this, so it is a consideration in the development of a new plant," he said, adding that the environmental impact of desalination has been well understood by the industry.
"Desalination plants... should only be constructed where they are found to meet a genuine need to increase water supply and are the best and least damaging method," the WWF report said.