The ministry 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", it said in a statement. Katerina Peristeri, the archaeologist in charge of the dig is to reveal her highly anticipated findings in two press conferences on November 22 and 29.
- Who could it be? -
The big question being posed by a fascinated Greek public, which has been following the dig daily, is: Who do the bones belong to?
The tomb's near-intact sculptures and staggering mosaics have been a cheering reminder to Greeks of past glories with the country today mired in economic woes.
Its sheer scale -- half a kilometre in circumference -- and the quality of the mosaics of a man driving a chariot and the abduction of Persephone by Pluto have fuelled theories that the tomb was built for a very high-status individual.
That hunch seemed to be confirmed Wednesday when Athens revealed that the tomb "used more marble than any other public building in ancient Macedonia".
"The extraordinary cost of construction means it is unlikely that it was built to bury a private individual," the ministry said.
Historian Miltiade Hatzopoulos, a specialist on the period, told AFP that all this suggested it contained a member of the Macedonia's famously fratricidal royal family.
The dynasty, which reached its zenith under Alexander (356-323 BC), was fabulously wealthy, but with all the gold came plotting, power-struggles and assassinations aplenty.
"We don't know where lots of the men in this family have been buried," said Hatzopoulos, who doubts that the macho Macedonians would have made the same effort for a woman.
Whoever the massive fourth-century BC structure holds, Hatzopoulos and other historians say it is highly unlikely to be Alexander himself, who conquered the Persian empire and much of the known world before his death at the age of 32.
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.
But the identity of the Greek tomb's occupant -- whose age and sex should normally be easily determined from the bones -- is not the only mystery surrounding the tomb.
- Cliches challenged -
"Why has this funerary monument, whose size makes it unique in the Hellenistic world, not been mentioned in any historical document?" one archaeologist, who did not want to be named, asked.
Experts have known about the tumulus -- which is 30 metres (100 feet) high -- since the 1960s, but work only began in earnest there in 2012.
What the team of archaeologists have turned up though has left more than one expert perplexed.
"An entrance crowned with a sphinx, sculptures like the caryatids, or the mosaics: we haven't seen this in a tomb before," said Alexandre Farnoux, director of the French Archaeological School of Athens.
The deliberate scattering of the bones and smashing of some of the objects inside the tomb also raises questions.
"Beyond the identity of the occupant, the real power of Amphipolis is to challenge the cliches of Greek art and to prove its capacity to produce the unexpected," said Farnoux.
As Greek TV and radio buzzed with news of the skeleton, archaeologists confirmed that another tomb close to where the treasure-filled burial chamber of Alexander's father Philip II of Macedon was unearthed in 1977 at Vergina, an hour and a half west of Amphipolis, has also survived the centuries intact.
And for the first time in six years of economic crisis, it is arguments between archaeologists rather than economists that are dominating the airwaves in Greece.