Specialist firm North West Marine was contracted so its drivers could search for the galleon which sank in Tobermory Bay in 1588.
However, businessman Matthew French, who contracted the firm for the venture, has now left the site amid allegations of he had missed a payment.
Tony Ratcliffe, managing director of North West Marine, and the company's consultant, David Wilkie, were alerted by staff on Mull that Mr French had left Mull..Mr Ratcliffe, 47, of Tobermory, said Mr French had missed his first payment on the contract and they had shut the operation down.
He alleged North West Marine is out of pocket for its divers' wages and other costs. He said it had nine divers diving daily for four weeks, completing almost 300 trips under the water.
Mr French, of the Poop Company in Somerset, had claimed to have secured cash from unnamed private investors for the dive and had a contract with the Duke.
In response to the allegations, Mr French said: "We left earlier than anticipated and we are not anticipating any more dives for this season."
Mr French declined to comment on whether the dive had suffered financial problems, adding: "It's unfinished business."