The Ocean Alert is owned by a company in Miami which recently raised a record haul of silver coins from a shipwreck.
Spanish authorities suspect the discovery might have been made in their territorial waters.
But Gibraltar disputes the claim, saying the ship had been boarded in international waters.
The Ocean Alert was stopped and boarded by Spanish police after leaving the British colony last Thursday.
It was then escorted to the Spanish port of Algeciras, where crew members were searched and computer equipment confiscated.
Acting on the orders of a judge, the police were hoping to pinpoint the location of a shipwreck which in May yielded half a million silver coins, worth $500m (£244m).
The salvage company has refused to say where it made the haul - which was promptly transported to the United States.
Initial speculation held that it was found off the coast of Cornwall in south-west England.
But the BBC's Steve Kingstone in Madrid says some politicians there suspect the mysterious wreck is of Spanish origin, or was found in Spanish territorial waters.
Neither the police nor the vessel's American owners - Odyssey Marine Exploration - will confirm what, if anything, was found during the Spanish search. But the answer is probably very little, our correspondent says.
The American crew of the Ocean Alert were expecting to be stopped and even had a lawyer on board, he says.
It is understood that some confiscated items, including computer hard drives, have yet to be returned.
Güncelleme Tarihi: 18 Temmuz 2007, 12:47
The dispute became a three-way diplomatic incident when Britain complained to the Spanish foreign ministry, arguing that Madrid did not have the right under shipping laws to intercept a vessel in international waters.
For now, the Ocean Alert remains in Algeciras and is expected to leave port after completing routine paperwork.
Spain has launched legal action over the treasure and the wreck.
But some experts believe it to be the Merchant Royal, an English ship carrying stolen Spanish treasure which sank in 1641.
US coin expert Dr Lane Brunner has said there is evidence the shipwreck was found off England's Cornish coast.
Odyssey has kept the location of its find secret, citing security and legal reasons.