The three nations posted the highest number of road deaths per million people in 2006, said the European Transport Safety Council, adding that the 27-nation bloc is unlikely to meet its goal of halving road deaths by 2010.
"We need a new, fresh impetus in all countries if we want to make up for this delay and deliver what the citizens of Europe deserve, a safe and sustainable road transport system," said the study.
Statistics compiled from EU and national agencies also showed that deadly road accidents rose in Estonia, Bulgaria, Romania, Hungary and Lithuania between 2001 and 2006.
Tiny Malta, followed by the Netherlands and Sweden posted the lowest number of deaths per million inhabitants in 2006.
Lithuania was found to be the worst, with 223 deaths per million people, while Malta had only 27 deaths and the Netherlands only 45 last year.
The most progress in improving road safety was in Luxembourg, France and Portugal, where new safety measures and campaigns were credited for a drop of between 42 percent and 47 percent in road deaths, the study said.
Altogether, about 39,200 people died on European roads last year.
The report said countries with the best safety records also had the best policies on curbing drinking and driving, speeding and stricter rules on the use of seat belts.
It pointed to the introduction of automatic speed control cameras as a major reason why road accidents decreased on French highways.
A similar report released by the Paris-based International Automobile Federation last month warned that road deaths were rising across the continent.
The EU is aiming to halve roadway fatalities in the union from about 50,000 in 2000 to 25,000 by 2010.
To reach this goal, EU Transport Commissioner Jacques Barrot has called on EU governments to adopt more EU-wide safety standards and new technologies.