Thirty years ago off the coast of Kent, beneath some 50ft of water, the prow of the 17th-century warship Stirling Castle emerged from a sandbank. It had been entombed by the Goodwin Sands for 300 years until the current changed. Soon, enough sand had been scoured away to reveal the entire hull. When she was discovered in 1979 her timbers looked as strong as the day they were hewn. Now she lies disintegrating.

The Stirling Castle is one of ten wrecks identified in English Heritage's new Heritage at Risk initiative, but lack of funds has meant that archaeologists can only watch as the sea reclaims the past.

Britain's ships made her great. We honour them by letting them rot, and pat ourselves on the back for doing so. Britain's navies pushed back the frontiers of the map, shaped world trade and fought epic sea battles. We are proud of our maritime past - except when it comes to looking after the shipwrecks that embody it.

Only 60 of the 32,000 wrecks around UK waters are protected by English Heritage. Despite the high cost of working underwater they receive a total of ony £450,000 a year. By comparison, Britain's 14,500 listed places of worship get more than £8 million (on top of £15 million from the Heritage Lottery Fund). The chosen wrecks - selected mainly on the basis of age, rarity and historical importance - are legally shielded from the predation of divers and salvage crews such as those who pulled two rare bronze cannon from HMS London, a 17th-century warship in the Thames. But the wrecks now face a different threat.

The sea preserves shipwrecks like volcanic ash preserves Pompeii and Herculaneum. Once on the seabed, the hull settles into the sediment, cutting off the oxygen and preventing decomposition. Mummified by mud, the ship is delivered to us centuries later, often with every mark of a carpenter's tool visible in its woodwork. Open the seal and the spell is broken - oxygen starts the countdown to destruction.

So let sleeping ships lie, runs the English Heritage mantra. But the marine environment that has preserved them is now changing. Unseen from the surface, the impact of development is spreading across the seabed. Offshore wind farms, subsea cables, oil-rig installations, mining and harbour developments are all shifting water-flows around our coasts, sculpting the seabed afresh in ways that are still little understood. Trawlers plough the seabed, tearing up timbers as easily as deepwater corals.

Odyssey Marine Exploration, a Florida-based treasure-hunting company that last year found a £250 million hoard of gold and silver coins a mile under the Atlantic, has recently set up shop in Falmouth, Cornwall, and has been searching the approaches to the Channel for wrecks. Almost every site it finds has been disturbed by trawlers.

In situ preservation of wrecks is preferred by English Heritage and Unesco's Convention on Underwater Cultural Heritage, which sets the agenda for maritime archaeology, because full-scale excavation is so expensive. Fewer than five wrecks have been fully excavated in the UK since the Mary Rose. A trickle of surveys and partial excavations continues, but many maritime archaeologists who dreamt of contributing to knowledge of Britain's greatest era find themselves merely curators of a decaying, unexplored national treasure.

Shipwrecks can entrance and educate. Almost eight million people have flocked to see the Mary Rose. Titanic broke box-office records and exhibitions of the liner's contents made millions. But academic pride prevents fascination from translating into funding for scientific projects. Collaborations between underwater archaeologists and businessmen usually end in disappointment. But every decomposing wreck is a good reason for academia to work with private enterprise.

Commercial archaeology companies are often attacked on ethical grounds, not because their methods are faulty. Trading in shipwreck artefacts is equated to handling stolen goods, no matter what their provenance. The National Maritime Museum once found itself in hot water from the International Council of Museums for displaying objects from the Titanic.

Odyssey Marine Exploration has the ambition, funding and technology to investigate shipwrecks all year round, to depths of more than a mile. They should be looked on as partners, not pariahs.

But Britain is considering signing the Unesco convention making it illegal to sell anything from under the water that is more than 100 years old. The instinct to regulate is justified - salvage without archaeological consideration (as happened with the cannon of HMS London) is like burning pages of a history book - but prohibition is unworkable. Maritime archaeologists are paralysed by lack of funds and the clock is ticking for our shipwrecked history.

Pride in our seafaring could help to fund archaeology. Collectors could help to finance academics to explore the history that surrounds our coast, not just be witnesses to its slow erosion.

Frank Pope is ocean correspondent of The Times

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