Mystic — Repairs to the schooner Amistad have turned out to be more expensive and time-consuming than originally predicted, according to the chairman of Discovering Amistad, the new nonprofit organization that owns the boat.

Len Miller of Essex said that after the boat was removed from the water in December and placed in the Mystic Seaport shipyard where it was built in 2000, it was discovered that the boat had never been re-caulked, which should have been done every six to seven years. In addition, both of the schooner’s Caterpillar diesel engines had to be replaced.

He said it was then that "our worst fears were confirmed that the boat was not maintained properly."

He said the repairs, which had been estimated at $300,000, cost $500,000. The state recently appropriated an additional $287,000 in bonding to help Discovering Amistad cover the additional cost.

Last year, the State Bond Commission approved a $762,000 grant for the organization so it could buy the ship for $315,000 and make repairs.

Miller said he was told by experts that both problems could have been avoided with proper maintenance by its previous owner, Amistad America.

On Monday, the boat was briefly put in the water following the caulking work but had to be removed because of leaky fittings. Plans are to put the boat back in the water Tuesday.

Miller said Sunday night that he hopes the boat will be ready to begin operation in mid- to late July, making visits to New London, Bridgeport and New Haven. The organization hoped to have already been underway.

A court-appointed receiver sold the schooner last fall to Discovering Amistad for $315,000. The sale came after the state had audited financially troubled Amistad America and took control of the ship.

The audit occurred after state Rep. Diana Urban, D-North Stonington, continued to raise questions about how the organization had spent $9 million in state funding.

When Amistad America ceased operation, it owed more than $2 million to a long list of small businesses, organizations, banks, individuals and other creditors who were never paid back.

The state had continued to fund Amistad America even after it fell deeper and deeper into debt while providing little documentation about how it was spending state funding.

Miller is keenly aware of the need to overcome that history. He wants the ship to be in perfect working order and boast a quality educational program when it sets out.

“We want to tell everyone we’re not the old organization," he said. “I’ve been involved in startups before, but this is different. Not only do we have to say who we are but who we aren’t. We’re not them.”

Unlike Amistad America, which took the ship to the Caribbean, Bermuda, Africa and Europe, Miller said the state’s flagship will now spend most of its time along the Connecticut coastline with a renewed educational mission.

Twenty five years ago, Miller founded SoundWaters, a Stamford-based nonprofit organization that provides educational programs about the environment of Long Island Sound to more than 27,000 students in Connecticut and New York each year while the schooner SoundWaters conducts 250 educational sails annually.

Miller said that with the caulking completed, the organization is waiting the delivery and installation of the new engines. He said four full-time employees continue to work on other aspects of the schooner, which will also have to be re-rigged.

He said the good news is that Discovering Amistad continues to develop an educational plan and is completing its strategic plan.

He said the organization is reaching out to city officials and nonprofit organizations in New London, Bridgeport and New Haven to develop community partnerships and reintroduce the boat to the public.

While the state will provide $294,000 in operational funding in each of the next two years, Miller said he hopes that the organization will need less state funding as it starts to raise its own revenue.

But, he said, the boat has to prove that it’s viable by being in operation and providing educational programs before it can seek out private funding.

j.wojtas@theday.com