"I think it's extremely important that there be cooperation between the two countries," Barry Clifford said on Wednesday after a press conference here in which he formally announced the discovery.
Clifford said the wreck found in just six metres (about 20 feet) of water "is most likely the Santa Maria".
"You got to look at the record: What are the chances another ship would be there? We've eliminated all the other spots. There's no other record of a ship from this area sinking in the bay of Cape Haitian from the early 15th century," the 68-year-old explorer said.
When asked about any prospective salvage claim that could be presented to the Spanish government to take possession of the wreckage, he expressed confidence that "Spain will support this fully and help Haiti".
Clifford said the wreck, which was found in 2003, but the importance of which was not understood until 2012, had been looted recently, with one cannon, several gun carriage wheels, parts of the helm and pieces of bronze used to keep the ship's frame together being removed.
"This is an emergency situation. The ship needs to be excavated as quickly as possible," he said.