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."

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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.

Treasure chest

But if the discovery of the ancient port of Constantinople promises a treasure chest of riches for historians and archaeologists, it also brings its problems. The old harbour straddles what is to become the biggest railway station in Turkey, a gleaming modern temple connecting the city's new high-speed rail and metro.

"It's a phenomenal site. But it opens a can of worms," said Mr Pulak. "This is to be the biggest station in Turkey and they'll be wanting to put huge shopping malls on the top."

The Yenikapi site is the linchpin of what the Turkish government dubs the "project of the century". The $4bn (£2.2bn) Marmaray transport project is being built by a Japanese-led consortium. There will be tunnelling under the Bosphorus for the first time ever, with high-speed trains going through the deepest underwater tunnel in the world in the middle of a high-risk earthquake zone. The tunnel itself will be built to withstand quakes of 9.0 on the Richter scale in the area of the North Anatolian Fault, which runs below the Sea of Marmara nearing the walls of Istanbul. Seismologists say a large earthquake and a mini tsunami are almost inevitable within a generation at the latest.

The ambitious new transport system is to shift 75,000 passengers an hour and to put Istanbul behind only Tokyo and New York in the global league table for urban rail capacity.

There is no doubt the Marmaray is needed urgently. In a city of 12 million, which seems to grow by the week, the traffic congestion is a nightmare and the Bosphorus bridges are gridlocked semi-permanently. So the engineers, transport officials and urban planners are in a hurry to get the infrastructure built by the end of the decade. That puts Mr Gokcay and his teams of experts under immense pressure to finish their dig.

"The transport guys say they are losing a million a day because of the archaeological delays," said one expert. "But it's ridiculous - when they were building the Athens metro the excavations took seven years. Here they want it finished in six months."

Ismail Karamut, the director of the city's museum of archaeology and a leading expert on the history of Istanbul, refuses to be intimidated by the urban planners. "This city is 2,800 years old and here we're digging right in the middle of a living city. It's not like excavating on a mountainside. The transport people can't start until we're finished. And maybe they'll have to change their project depending on what we find. We've told them we can't give them a deadline."

It is perhaps logical and fitting that the same spot that provided the shipping hub for 5th-century Constantinople should become the rail nexus for 21st-century Istanbul. But the dilemmas thrown up by trying to secure the future without destroying the past are a headache.

Ottoman gardeners

The discovered artefacts fall into the easy bit. The ships can be rebuilt using computer simulations; the anchors, ropes and coins can all be housed elsewhere. But you cannot move the ancient port - believed to be Portus Theodosiacus, in use from the 4th to the 7th centuries, after which it started silting up, then became useless for shipping. In later centuries it served just as fertile vegetable plots for Ottoman allotment gardeners.

One idea is to cordon off the old port area creating an "archaeological island" that would be an exhibit in the new transport complex. But that is a tricky solution because of the underground shafts and the vast scale of the station.

The doyen of archaeology for Constantinople, the late German researcher Wolfgang Muller-Wiener, predicted 30 years ago that the old port would be found at Yenikapi. But the site was covered in illegal tenements and could not be explored. It was the modern transport project that made discovery of the old port possible, since the site had to be cleared to make way for the railway station.

Mr Karamut said: "We knew from the ancient documents and records that there was some kind of port around there. But we didn't know exactly where. We didn't know that it could be Constantinople's first harbour."