Archaeologists from the Mary Rose Trust are to manage the excavation of part of the medieval ship found in Newport last summer.
The ship's bow and stern are still on site
Archaeologists from across Europe will be attempting to reclaim as much of the ship as possible but said they will leave the stern because it's felt, it is too dangerous to dig out.
This has angered Newport-based activists from the Save Our Ship campaign who say that without the stern, they will not get a complete picture of what the ship looked like.
The discovery of the ship last summer - which contains vital clues about Wales' early sea trade with Europe - has been hailed as a major discovery.
But the efforts to unearth the vessel has met with a succession of problems.
Before the Mary Rose Trust got involved, Gwent and Glamorgan Archaeological Trust (G-GAT) was working on the excavation.
However, they stopped work after getting into a dispute over payments from Newport council.
Charles Ferris from Save Our Ship told BBC News Online: "If we don't save it, there is going to be a loss to mankind.
Charles Ferris, from Save Our Ship
"We're appalled that this crucial section of the ship will not be saved.
"If we don't get the stern out, we'll never know how the ship was sailed."
The group is now calling for an independent report into the site.
"If they're worried about health and safety, why don't they use a mechanical grab?" he asked.
A spokeswoman for Newport Council said the people in the Mary Rose Trust were internationally renowned for their work.
"This is the advice that they have given us. We're going along with what engineers and archaeologists are saying.
"There are real, real, safety issues."
Work at the ship excavation
The ship was uncovered when work began on an arts centre for the city.
Tests established it was built in the 15th century, with wood from the nearby Forest of Dean used in its construction.
Thousands of people visited the site to view the ship, and joined the campaign to have it recovered.
Parts of the ship which have already been removed are being stored in water tanks at Llanwern steelworks.
The aim is to reconstruct as much of the 65-foot ship as possible to put it on display to the public.
Artefacts such as pottery, cloth and shoes have been found on the ship, along with human bones.