The remains of the ship, known simply as the Swash Channel Wreck, were preserved for centuries under the seabed in six metres of water off the Dorset coast.
But now its ornately carved timbers, the earliest still in existence in Britain, are being eaten away.
The sand that protected it has been shifted by changing currents and tides, leaving the 40m vessel's timbers exposed to bacteria and the tunnelling of aquatic shipworms.
David Payton, senior lecturer in marine archaeology at the university, told the Independent on Sunday: "The damage there has increased dramatically since we first started studying it. It's a race – you've only got a certain amount of time before it's too late and there's no point.
"It's been buried until now, but in the last four or five years it's become exposed. The longer the wreck is exposed, the more damaged it will be. If nothing were done within the next five years there'd be nothing left."
Tests on the timbers and artefacts trace the ship's history back to Europe in the early 1600s, where it was probably engaged in the beginnings of international trade with the Far East.
Dating evident recovered includes Rhenish stoneware dated to around 1600 – 1620 and Dendrochronological work undertaken by Nigel Naying of Lampeter University has provided a felling date for a single timber of post 1585.The evidence to date suggest a that the wreck is of a relatively, for the period, high status ship.
It has been suggested that re-burying the wreck would help to preserve it, but as this is one of the busiest shipping lanes in the country, that could prove difficult. The only option left would be to raise some of it to go on show in a museum. But that is expensive and time consuming. It has taken years to treated the timbers of the Mary Rose to get them to a point where they could go on show.
The latest efforts to preserve the wreck will be featured in an episode of Paul Rose's new BBC2 series Britain's Secret Seas.
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