Spurred by government subsidies, energy companies became so enthusiastic that they designed generators that ran exclusively on the oil, which in theory would be cleaner than fossil fuels like coal because it is derived from plants.

But last year, when scientists studied practices at palm plantations in Indonesia and Malaysia, this green fairy tale began to look more like an environmental nightmare.

Rising demand for palm oil in Europe brought about the clearing of huge tracts of Southeast Asian rainforest and the overuse of chemical fertilizer there.

Worse still, the scientists said, space for the expanding palm plantations was often created by draining and burning peatland, which sent huge amounts of carbon emissions into the atmosphere.

Considering these emissions, Indonesia had quickly become the world’s third-leading producer of carbon emissions that scientists believe are responsible for global warming, ranked after the United States and China, according to a study released in December by researchers from Wetlands International and Delft Hydraulics, both in the Netherlands.

“It was shocking and totally smashed all the good reasons we initially went into palm oil,” said Alex Kaat, a spokesman for Wetlands, a conservation group.

The production of biofuels, long a cornerstone of the quest for greener energy, may sometimes create more harmful emissions than fossil fuels, scientific studies are finding.

As a result, politicians in many countries are rethinking the billions of dollars in subsidies that have indiscriminately supported the spread of all of these supposedly eco-friendly fuels for vehicles and factories. The 2003 European Union Biofuels Directive, which demands that all member states aim to have 5.75 percent of transportation run by biofuel in 2010, is now under review.

“If you make biofuels properly, you will reduce greenhouse emissions,” said Peder Jensen, of the European Environment Agency in Copenhagen. “But that depends very much on the types of plants and how they’re grown and processed. You can end up with a 90 percent reduction compared to fossil fuels — or a 20 percent increase.”

He added, “It’s important to take a life-cycle view,” and not to “just see what the effects are here in Europe.”

In the Netherlands, the data from Indonesia has provoked soul-searching, and helped prompt the government to suspend palm oil subsidies. The Netherlands, a leader in green energy, is now leading the effort to distinguish which biofuels are truly environmentally sound.

The government, environmental groups and some of the Netherlands’ “green energy” companies are trying to develop programs to trace the origins of imported palm oil, to certify which operations produce the oil in a responsible manner.

Krista van Velzen, a member of Parliament, said the Netherlands should pay compensation to Indonesia for the damage that palm oil has caused. “We can’t only think: does it pollute the Netherlands?”

In the United States and Brazil most biofuel is ethanol (made from corn in the United States and sugar in Brazil), used to power vehicles made to run on gasoline. In Europe it is mostly local rapeseed and sunflower oil, used to make diesel fuel.

In a small number of instances, plant oil is used in place of diesel fuel, without further refinement. But as many European countries push for more green energy, they are increasingly importing plant oils from the tropics, since there is simply not enough plant matter for fuel production at home.