The practice of "fuel tankering" saved money by avoiding higher prices at other ports, but drove up carbon dioxide emissions by 18,000 tons last year, a BBC investigation reported.
Cost savings, the report said, can range from about $13 to $130. But the added emissions for European routes could be equivalent to a town of 100,000 people.
The report called into question the airline's commitment to addressing climate change.
The airline's parent company, International Airlines Group, has made a commitment to become the first airline group to commit to net zero emissions by 2050.
Greenpeace U.K. Executive Director John Sauven told BBC News fuel tankering is a "classic example of a company putting profit before planet." The airline had been treating climate change "like a PR problem," he added.
"This is why we need government-enforced reduction targets to ensure airlines take responsibility for the damage their emissions are causing."
IAG CEO Willie Walsh said the airline is now reassessing its position.
"Clearly the financial savings incentivize us to do tankering. But maybe that's the wrong thing to do," he said.
