The world’s largest ever search for Christopher Columbus’ long-lost flagship, the Santa Maria, is about to be launched by the United Nations’ cultural and scientific organisation, Unesco.

The initiative has been triggered by the underwater exploration work carried out off the north coast of Haiti by the American explorer Barry Clifford, who announced in May that he had discovered what might be Columbus' long-lost vessel.

Unesco – which has now examined Clifford’s wreck – believes that it is not the Santa Maria, but that the real final resting place of Columbus' flagship could be relatively nearby.

The Paris-based organization now plans to look for the Santa Maria in a number of different locations – some on land and others on the seabed.

Both the nature of Unesco’s outright rejection of Clifford’s site, and some of the organisation’s proposed alternatives, are likely to prove controversial.

An official Unesco report issued today largely ignores 11-year-old photographic evidence for what could be Columbus-era cannon on the site. The cannon have tragically been looted since the photographs were taken but some of the world’s top experts in early ordnance who have looked at the photos believe that they are 15th or 16th century weapons, sometimes known as lombards.

The report also ignores crucial evidence from an expedition which almost certainly visited the site in 1960. It also admits that no tests, which could have revealed the geographical origin of the vessel, have been carried out on the ballast from the wreck. Likewise no detailed analysis has been carried out on the bronze objects found on the site – tests which might have revealed the objects’ ages. Neither does the report really assess in any detail the case for there potentially being two wrecks, one early and one later, on the site, rather than just one.

The bronze items – a number of ship construction fasteners – is the main reason for rejecting it as the Santa Maria. Unesco says that ship construction fasteners only came into use in the late 17th century, a belief based mainly on the fact that such fasteners have apparently not been found so far on earlier wrecks.

Very significantly, Unesco also seems to have moved towards the belief that the Santa Maria may be buried under sediments on what used to be seabed and is now coastal marshland.

Many scholars are likely to be very critical of any plan Unesco has to look for the Santa Maria in those marshes, because, they argue, Columbus's vessel could not have reached them due to some shallow and dangerous reefs. Unesco’s only argument for looking on land, and one of only two arguments for rejecting Mr Clifford’s site, is a short very ambiguous passage in an edited version of Columbus’ diary. Sadly only edited versions survive.

Unesco seems to think that the remains of the Santa Maria could be buried in one of two areas of marshland along the North coast of Haiti, near the small town of En Bas Saline, or alternatively near La Petite Anse. The official Unesco report says that “the Santa Maria might indeed now” lie “under coastal sediment”.

A painting of the ‘Santa Maria’ caught in a storm off the coast of Hispaniola in 1492 (Alamy)

It added: “To better estimate the location of the wreck of the Santa Maria, it will be important to understand more precisely the geomorphological evolution of the coastline.”

The Unesco report may also have implications for the US public’s perception of the organisation; America’s relationship with Unesco is currently very poor.

The United States has refused to pay its set financial contribution to Unesco for the past three years – and last year the organisation stripped America of its Unesco voting rights.

The Santa Maria saga could potentially further damage relations, or at least public attitudes, because a senior US underwater archaeologist, Professor Charles Beeker of Indiana University, who had been conducting a preliminary investigation of the site earlier this year at the request of Barry Clifford, has been refused permission to continue his work. What was in effect a US-led investigation has been more or less killed off by Unesco, and replaced by a partly European team.

Unesco has officially advised the Haitian government against accepting the US archaeological team’s proposal because “in its current state” it “lacked many elements required for the appropriate underwater archaeological research on the concerned site”, and because it “did not conform" to the organisation's standards on the protection of underwater cultural heritage.

The Santa Maria was the flagship of Christopher Columbus’ three-vessel fleet which discovered the New World. The fleet first reached the Americas on 12 October 1492 when they sighted the Bahamas. 75 days later, at around midnight, while Columbus was asleep, the Santa Maria drifted onto a reef and could not be refloated. Within a few hours the ship’s seams began to open – and the interior of the vessel was flooded.

Christopher Columbus hired the ship in 1492 and sailed in it from southern Spain’s Atlantic coast in search of a new western route to Asia (Rex)

However, Columbus and his crew were made welcome by a local Taino chieftain. Columbus then established a fort, left a garrison of 39 men there, and returned to report his discoveries to the King and Queen of Spain. Later in 1493, he returned to his fort in Haiti – but it had been destroyed and the garrison had all died or been killed.

In an official statement, Unesco said that "the evidence collected concerning the location, nature and artifact content" of the site has been "subjected to thorough investigation by an acclaimed team of experts".

Professor Beeker still thinks that Clifford’s site is of potential importance.

“I think that Mr. Clifford’s site is still the best candidate yet proposed for the wreck of the Santa Maria,” he said. “I am not saying that it is definitely Columbus’ flagship, but without a more thorough and comprehensive investigation, the site cannot be discounted.”

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“But even if it ultimately turns out not to be the right site, all the historical and other evidence points to the vessel having been wrecked in that immediate area – certainly within just a few hundred metres of Clifford’s site. Unfortunately Unesco’s ideas as to where the wreck of the Santa Maria may lie are extremely flawed.

“Their suggestion that it could lie on what is now land is not consistent with contemporary accounts suggesting the wreck’s considerable distance from the shore.

“In my view it would have been impossible for the Santa Maria to drift onto what is now land – because the vessel would have been wrecked on the reef before getting that far, which is precisely what happened.

“The bronze fasteners are a puzzle – but not sufficient reason on their own to dismiss the site without detailed investigation. There are a number of possible explanations for the presence of those bronze objects. The fact that bronze fasteners have not yet been documented on the few known early Iberian Atlantic shipwrecks does not mean that there were no such ships from that time period that used bronze fasteners.

“Mr Clifford has triggered very substantial renewed international interest in finding Columbus’ lost flagship – a vessel which represented the start of continuous contact between the old and new worlds, and one if not the most important event in world history.”

Reacting to the Unesco report, Mr Clifford, said: “It is essential that Unesco investigates the entire area where the lombard cannons were. I would be delighted to assist them and look forward to them getting in touch.