It said the process would also benefit fishermen, identifying wrecks of non-archaeological value which could be safely fished.
The loss of expensive fishing equipment would also be minimised, said their report.
But trawler crews have disputed the claims they are to blame and questions have also been raised by some sceptics because the research was carried out by a US salvage company, which makes money selling sunken treasure.
Christopher Vinnicombe, of the Cornish Fish Producers' Organisation, said they tried to avoid the "thousands" of wrecks in the Channel because it often damaged their equipment.
Greg Stemm, head of Odyssey Marine Exploration - which carried out the survey - told BBC's Newsnight he saw no problem with expecting a return on money invested in discovering shipwrecks, as would happen in other fields of research.
The major pressures on shipwrecks were damage from trawlers, scallop dredges and natural causes, its research found.
The survey explored the western English Channel and the Western Approaches, a rectangular area of the Atlantic ocean lying on the UK's west coast.
Marine archaeologist Dr Sean Kingsley, director of Wreck Watch International, said it was vital that some of the more historically important wrecks received greater protection.
"The English Channel is the British Museum of the deep," he said.
"Everything is down there, jewellery, musical instruments; the artefacts contained in the wrecks helps us to build a picture of what society looked like."
'Dredges like bulldozers'
He told the BBC, Unesco's preferred option of preserving wrecks in situ on the sea bed was a "fair enough ideology" but there were certain important wrecks that needed to be taken "out of harm's way".
"Trawlers and scallop dredges are bulldozers of the deep, as they go along the sea bed they literally plough it."
He said they had teeth and chains designed to extract scallops and to drive flatfish into nets, which were "grinding away the archaeology" and exposing remains.
He said while conservationists and biologists had known about the damage to marine environments caused by these techniques for some years, but nobody had considered the effects on old shipwrecks.
"The damage is so severe to a number of the wrecks we saw that they may not be there in five to 10 years' time."
Newsnight: Channel shipwrecks revealed
Wreck Watch said it believed HMS Victory was at extremely high risk, with rich archaeological artefacts, delicate hull timbers and even human bones vulnerable to total destruction.
Each year, global trawling by the fishing industry covers an area of seabed as large as Brazil, the Congo and India combined, with the upper 2.4in-7.9in (6cm-20cm) of the seabed ploughed to extract scallops and drive flatfish into nets often weighing up to eight tonnes.
Shipwrecks are also environmentally important, because they offer rich habitats providing shelter, feeding and nesting for fish.
Destruction is caused when fishing boats cut furrows into shipwrecks, loosen archaeological deposits, drag artefacts from sites, expose wrecks to oxygen, and break up wooden structures allowing objects to be washed away by currents.
Other wrecks identified in the survey include a 30-metre long merchant vessel lost around the middle of the 17th century with a cargo of elephant tusks, a consignment of iron cannon and copper 'manilla' bracelet money.
Discovered at the site was possibly the oldest carpenter rule in existence featuring a logarithmic scale.
Also there is the wreck of the 22-gun Marquise de Tournay, a French ship captured and sunk by the British in 1757, believed to be on its way back from North America and the Caribbean.
It is the only wreck of a merchant vessel of this period trading with the Americas found in European waters.
The wrecks of HMS Victory and the Marquise de Tournay lie within the most heavily fished section of the survey region, said Wreck Watch.
Seven WWI and WWII submarines are also in the area.
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