- Prehistoric collection (east wing)
This unit covers the Late Neolithic period and Bronze Age. It contains early vases with engraved decoration from the island of Gavdos, cave finds which display Helladic and Cycladic influence, clay Linear A and B tablets, clay roundels, a collection of fine gold necklaces, seal-stones, clay sealings, stone beads, a group of relief plaques made of hippopotamus ivory from Minoan tombs, and the famous series of pottery vessels produced locally in Chania, including a fine pyxis with representation of a musician. The Minoan clay larnakes and large pithoi, which were used for storage or burials, are especially impressive.

- Antiquities of the Historical period (west wing)
A variety of objects dating to the Historical period are presented here: Geometric (tenth to eight centuries BC) vases, figurines, weapons and jewelry, mostly from cemeteries; a fragment of an early seventh century BC Archaic frieze from Chania; pottery, sculpture and stone inscriptions; Roman floor mosaics of the second and third centuries AD, with Dionysiac scenes and episodes of the myth of Poseidon and the nymph Amymone; also, an excellent Roman statue of the Cretan philosopher Elyros.