The EFSA said an initial review showed that the "design, reporting and analysis of the study ... are inadequate," meaning it could not "regard the authors' conclusions as scientifically sound."
Given these shortcomings, the EFSA called on the author of the study, French scientist Gilles-Eric Seralini, to provide additional information before a second, final review is completed by the end of this month.
Seralini's team at France's University of Caen found that rats develop tumors when fed agribusiness giant Monsanto's NK603 corn, or when exposed to one of the company's weedkillers used with it, containing glyphosate.
The scientist insisted he would not give the EFSA any additional information until it first detailed the basis of its own assessment.
"It is absolutely scandalous that (EFSA) keeps secret the information on which they based their evaluation" of NK603 and the pesticide, he said.
"In any event, we will not give them anything. We will put the information in the public domain when they do," Seralini told AFP.
NK603 was developed by Monsanto to make it resistant to the Monsanto herbicide Roundup, enabling farmers to use the weedkiller just once in the crop's life-cycle, enabling substantial savings.
Seralini and his team say their experiment in GM food is the first to follow rats through their lifespan, as opposed to just 90 days, but other experts have also questioned its methodology, results and relevance to humans.
EFSA, which reviews the use and authorisation of GMOs (Genetically Modified Organisms), said that "based on the information published by the authors ... it does not see a need to re-examine its previous safety evaluation of maize NK603 nor to consider these findings in the ongoing assessment of glyphosate."
In May, the EFSA said a temporary French ban on another Monsanto corn, MON810, was not properly based on scientific evidence.
"Based on the documentation submitted by France, there is no specific scientific evidence, in terms of risk to human and animal health or the environment," EFSA said of the French position.
France, like many EU countries, has a long record of opposition to GM foods but the pressures on farmers in terms of cost are immense, driving their increasing use, especially in emerging economies such as China and Brazil.
EFSA listed a series of concerns it had with Seralini's findings, among them that the type of rat used "in the two-year study is prone to developing tumours during their life expectancy of approximately two years.
"This means the observed frequency of tumours is influenced by the natural incidence of tumours typical of this strain, regardless of any treatment. This is neither taken into account nor discussed by the authors."
Environmental groups attacked the EFSA action, saying it was not doing enough on its own to test GM foods while condemning the work of others.
The "EFSA fails to convince us that they are putting public safety before the interests of agribusiness biotech industry," said Mute Schimpf of Friends of the Earth.
"Instead of dismissing peer-reviewed independent research they should be asking themselves why they don't demand long term safety tests for genetically modified foods," Schimpf said.