£2bn train tunnel linking Europe to Asia faces delays as dig unearths 5th-century port. Lost treasures of Constantinople test Turkey's 21st-century ambition

Deep in the soft black earth beneath the cleared slum tenements of old Istanbul, Metin Gokcay points to neatly stacked and labelled crates heaped with shattered crockery. "That's mostly old mosaics and old ceramics," said the Istanbul city archaeologist. "And over there we found bones and coins."

Looking at huge slabs of limestone emerging from a depth of more than 7 metres (25ft) below ground, he adds: "That's late Roman, this is early Byzantine. This tunnel here is very interesting. Perhaps Constantine's mother had her palace over there."

The archaeologist is making mischief. For more than a millennium this city bore the name of Constantine, but whether the emperor's mother lived at this spot called Yenikapi, a powerful stone's throw from the Sea of Marmara, is a moot point. Mr Gokcay is intrigued and baffled by the subterranean stone tunnel which, measuring 1.8 metres by 1.5 metres, is too big to have been used for sewage or as an aqueduct.

But if Mr Gokcay remains in the dark as to the function of the ancient tunnel, his excavations have led to a stunning discovery that could jeopardise Turkey's most ambitious engineering project - a new rail and underground system traversing the Bosphorus and connecting Europe to Asia via a high-speed railway.

Mr Gokcay has uncovered a 5th-century gem - the original port of Constantinople, a maze of dams, jetties and platforms that once was Byzantium's hub for trade with the near east.

Cemal Pulak, a Turkish-American, from Texas, and one of the world's leading experts in nautical archaeology, said: "The ships from here carried the wine in jars and amphorae from the Sea of Marmara. The cargoes of grain came in from Alexandria. This was the harbour that allowed this city to be."

In a mood of barely suppressed excitement, armies of archaeologists and labourers have been scraping away silt and rubble for the past year and revealed a vast site the size of several football pitches. It is slowly giving up its secrets and its treasures.

Seven sunken ships have already been found buried in mud at Yenikapi, a few hundred metres inland from the Sea of Marmara and a 10-minute stroll from the mass tourist attractions of the Grand Bazaar and the Topkapi Palace.

Mr Pulak is thrilled that one of the ships, a longboat, may be the first Byzantine naval vessel ever found. All of the boats appear to have been wrecked in a storm. There are 1,000-year-old shipping ropes in perfect condition, preserved in silt for centuries. There are huge forged iron anchors, viewed as so valuable in medieval Byzantium they were highly prized items in the dowries of the daughters of the wealthy.