It was the scientific surprise of 2012. Researchers announced they had found that long stretches of human DNA – previously dismissed as "junk" – were in fact crucial to the working of our bodies. The assumption that our cells are controlled by only a few genes was wrong.

Scientists on the Encode project – an international public consortium researching the human genome – argued that most of our DNA has a part to play.

But this idea is now the subject of an astonishingly vitriolic attack from other scientists, who say that Encode's "absurd" ideas are the work of people who know nothing about evolutionary biology. "News concerning the death of junk DNA has been greatly exaggerated," they insist.

The row divides scientists over the most fundamental of questions – is most of our DNA devoid of purpose or does it play a major role in our cells? The debate has been triggered by a critique in the Genome Biology and Evolution journal that is striking for its strident language.

"Everything that Encode claims is wrong. Their statistics are horrible, for a start," the lead author of the paper, Professor Dan Graur, of Houston University, Texas, told the Observer. "This is not the work of scientists. This is the work of a group of badly trained technicians."

The scientists responsible for Encode – whose findings were published in more than 30 papers in Nature, Science, Genome Biology and other journals last September – reject the criticisms.

"The nature of the attacks against us is quite unfair and uncalled-for," said Dr Ewan Birney, of the European Bioinformatics Institute, near Cambridge, a principal investigator in the five-year project. "Our work has very important implications for understanding disease susceptibility."

When the human genome was sequenced in 2000, only 26,000 genes appeared to be directing the manufacture of proteins and growth control, and 98% of our DNA was written off.

But Encode researchers claimed to have identified more than 10,000 new genes and suggested that up to 18% of our DNA is responsible for regulating other genes. They said about 80% of DNA had a biochemical function. The group also identified where defects in DNA could leave a person susceptible to illnesses such as Crohn's disease, diabetes and bipolar disorder, discoveries that could help treat such ailments.

This is dismissed as "absurd" by Graur and others, including scientists from Johns Hopkins University in Baltimore. They accuse Encode of using "analytical methods that yield biased errors and inflate estimates of functionality" and say it reveals a basic misunderstanding of evolutionary biology.

"Just because a piece of DNA has biological activity does not mean it has an important function in a cell," said Graur. "The Encode people don't seem to have grasped that point. They completely exaggerated the amount of human DNA that has a role to play inside our cells. Most of the human genome is devoid of function and these people are wrong to say otherwise."

The Encode project involved 442 researchers, based at 32 institutes, who used 300 years of computer time and five years in the lab to get their results.

Grauer said: "This is big science and big science should, if nothing else, generate masses of reliable data. They haven't done that. When they published their results, it was claimed its conclusions would necessitate the rewriting of textbooks. Well, yes, but only those textbooks about marketing, mass-media hype and public relations."

But Birney said: "I think this attack is really a complaint about big science, about big projects that absorb lots of money. These people don't like that."