Nine skulls and assorted bones have been unearthed in the last two days at the site, where builders were laying concrete foundations Friday afternoon.
Just a few paces away, vacationing families gawked at snow leopards and flamingos.
Resting on piles of bricks were two large, rust-colored skull fragments discovered Friday, after police had delivered remains found earlier to forensic experts who have begun an investigation, according to construction foreman Vladimir Allik.
Visible on at least two of the skulls were "holes that could be from bullets," said Igor Konyashkin, acting prosecutor for the Krasnopresnensky district, where the run-down zoo is located.
"There is a basis for suspecting that it is the result of Stalinist repression," police spokesman Igor Tsyryulnikov said of the grave.
Konyashkin said that while the find was curious enough to prompt police to investigate and prohibit further digging at the site, it was too early to pin blame on the NKVD, the KGB predecessor that killed millions under Stalin in the 1930s. The NKVD is known to have disposed of victims in at least 13 mass graves across Moscow.
"It often happens in Moscow that we find bones -- Stalinist and non-Stalinist," said Yury Smirnov, Moscow's top investigative prosecutor.
A leader of Memorial, the group dedicated to uncovering and documenting Soviet repression, said the site lacked the earmarks of an NKVD grave.
Alexander Milchakov said NKVD officers had "strict orders" to shoot victims in the nape of the neck, leaving a neat exit wound in the forehead. The apparent bullet holes in the skulls found in the zoo were in the temple area, according to foreman Allik.
Milchakov, who has worked with the government since 1991 to uncover mass graves, also said that the NKVD usually worked on a much larger scale. The NKVD secretly buried over 1,000 people under paths at Vagankovskoye Cemetery, cremated tens of thousands at Donskoye Cemetery in central Moscow and interred up to 300,000 at Butovo, just south of Moscow.
Even if the Moscow Zoo bodies prove to be victims of Stalin, Milchakov said, the site's exotic location was an exception.
"I don't think the NKVD in those years had such a lack of resources that they had to climb into a tiger's cage to dispose of their victims," he said. "They had their own methods, which were neater and more effective."
Irina Kostina, a lecturer at the zoo, said the area where the bones were found had been in the 1930s a little-used park-like area of the zoo.
Allik said the bones were discovered all jumbled together, and in some cases skulls were found far away from any other bones.
"Chaos," he said, surveying the site. He added that he feared he would find more bones when digging resumed.
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