Russia failed to comply with a human rights obligation to provide evidence, the Strasbourg judges ruled.
Soviet Russia only admitted to the atrocity in 1990 after blaming the Nazis for five decades.
But the ruling also said the court had no authority to rule on the killings.
The massacre in Katyn forest took place before the European Convention on Human Rights was signed.
The court’s examination came after 15 relatives of the victims claimed that Russia had failed to carry out an adequate investigation.
They said Moscow had prevented them from finding out the truth about the killings in western Russia.
Moscow started a criminal investigation into the killings the same year, but the inquiry was discontinued in 2004 on the orders of the Russian chief military prosecutor’s office.
Files about that decision remain classified, and the Polish claimants have not had access to it or any other information about the investigation.
No-one has ever been convicted in connection with the massacre, with Russian prosecutors arguing that those responsible are now dead.
However, in 2010 Russia’s parliament issued a statement saying more work needed to be done in “verifying the lists of victims… and uncovering the circumstances of the tragedy”.
The parliament also said the killings had been carried out on Soviet leader Joseph Stalin’s orders.
In 2010, Russia also published online six once-secret files on the mass killings. The documents had until then only been available to researchers.
Poland has repeatedly demanded that Russia open all its files on Katyn.
The killings were carried out by the Soviet secret police (NKVD) in April and May 1940 in the Katyn forest near the city of Smolensk, and also near the village of Mednoye, in the Tver region, and the village of Pyatykhatky in what was then Soviet Ukraine.
The victims were members of the Polish elite, arrested after the USSR invaded and annexed eastern Poland in 1939.
They were shot on the recommendation of NKVD head Lavrenty Beria, according to one of the published secret files.
In a letter to Joseph Stalin dated March 5, 1940, Lavrenty Beria says the Polish prisoners of war should be executed and refers to them as “steadfast, incorrigible enemies of Soviet power”.
“Each of them is just waiting for liberation so as to actively join the struggle against Soviet power,” it says.
The letter bears Joseph Stalin’s signature in blue pencil, with the comment: “In favor”.
In April 2010, Polish President Lech Kaczynski and more than 90 other government officials were killed when their plane crashed as it was trying to land at Smolensk airport to attend an event marking the Katyn massacre.
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