Rita Gardner, the director of the Royal Geographical Society, said the figures underlined the need for the government's £2m Action Plan for Geography.
Dan Raven-Ellison, co-founder of the Give Geography Its Place Campaign, said the subject was under severe threat, adding that it had a poor media image and too few specialist teachers. "So many of the comments about geography teachers, for instance, are in the form of a joke that it makes it hard to persuade children that it is a crucial subject which helps them understand everything from flooding and climate change to immigration," he said.
The fall in the numbers taking geography came as Martin Rees, president of the Royal Society, said maths and science seemed to have turned the corner: "[These] results at last provide a suggestion that the health of mathematics and the sciences is beginning to improve."
However he warned that physics remained on the "critical list". "In actual terms, we're looking at just 98 more people taking the A-level compared to last year. We need more evidence before we can conclude with confidence that this is the beginning of a recovery," he said.
Yesterday's figures showed increases in the numbers studying German (1.6%) and Spanish (6.6%) and a slight drop in French (1.2%). Entries in chemistry were up 0.6% and physics by 0.4%, but biology saw a decrease of 0.6%.
English and maths were again the most popular choices, with an 8.3% increase in further maths and 7.3% rise in maths. John Dunford, general secretary of the Association of School and College Leaders, said many were choosing subjects based on future careers: "Student debt is so large at the end of university that students have become a lot more savvy about job prospects after their degree and clearly maths, physical sciences and modern languages give you a considerable advantage in the job market."
However, Richard Lambert, director-general of the CBI, said there were still too few studying science to meet the shortage of engineers and scientists: "We are facing a growing skills shortage in these areas that has serious implications for the future health of our economy. Numbers studying physics are little more than flatlining at a time when they need to rise sharply."
Yesterday's figures also revealed more pupils are taking an A-level in critical thinking and a fourth successive rise in the number taking religious studies.
Nick McKemey, the Church of England's National Schools Improvement Officer, said: "Religious studies is increasingly popular because students appreciate the importance of understanding the meaning of faith in Britain and the world today, whatever career they are seeking to pursue."