Officials said the remains were clearly those of "a powerful personality which can be seen from this unique tomb", with speculation rife that it could be that of Roxana, Alexander's Persian wife, his mother Olympias or one of his generals.
The skeleton will now "be studied by researchers", the ministry said in a statement. Katerina Peristeri, the archaeologist in charge of the dig at huge tomb near Amphipolis in northern Greece, is due to reveal the first of her highly anticipated findings on November 29.
Angelique Kottaridis, who is in charge of the dig at Aigai, modern Vergina, 180 kilometres to the west of Amphipolis, said it also dates from Alexander's lifetime, after breaking the news on her Facebook page Tuesday.
The near-intact sculptures and staggering mosaics found at Amphipolis have been a cheering reminder of past glories for a country mired in economic woes.
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The beauty of a sphinx and intricate mosaics of a man driving a chariot and the abduction of Persephone by Pluto have also fuelled theories that the tomb was for a very high-status individual.
After his mysterious end in Babylon he is said to have been buried in Alexandria in Egypt, the city he founded, although no grave has ever been found.