After a year of closed-door negotiations with developer Don Chiofaro and the New England Aquarium, city officials say it’s finally time to move forward with a skyscraper Chiofaro wants to build on the Boston Harbor Garage site.

The Boston Planning & Development Agency on Friday filed a plan with the state that should allow construction of a building as tall as 600 feet on a prime piece of waterfront land. It also requires Chiofaro Co. to set up a fund worth up to $30 million to compensate the nearby New England Aquarium for business it might lose during construction and once the tower opens.
In addition, the developer would have to permanently set aside parking for aquarium visitors and earmark $10 million for the aquarium’s proposed “Blue Way” open space on Central Wharf.

Chiofaro’s waterfront project would significantly alter the downtown skyline. The project — which at one point called for a pair of soaring towers — has been hotly debated over the last decade. It would be the first project in Boston for the colorful developer — who famously clashed over it with late mayor Thomas M. Menino — since he built International Place in the 1980s.

The plan still requires state approval, a process that will take about two months and involve another round of public comment. Then the building itself must go through city and state permitting — a process that will likely take many months more — before construction can begin.

But after lengthy negotiations — which followed years of public planning meetings over zoning on the downtown waterfront — the Walsh administration says it decided the time had come to push ahead, clearing the way for a project that would replace an old concrete parking garage with a signature tower on the skyline.

“This plan just needs to be approved,” said Rich McGuiness, deputy director for climate change and environmental planning at the BPDA. “We think this is pretty good to go.”

In a statement, the aquarium said the city’sterms “address the fundamental concern the New England Aquarium has consistently voiced regarding our financial viability,” and said it looks forward to working on a plan that increases access to the waterfront.Executives at the Chiofaro Co. expressed relief and said they look forward to making the tower a reality.

“Now we can shift our focus to the fun stuff,” project manager Rob Caridad said. “We have been in a planning process for five years. By laying this foundation, we can start thinking about doing what we’ve said we want to do: creating an iconic building on the skyline and a new public realm on the waterfront.”

The zoning plan covers a 42-acre stretch of the waterfront, from Long Wharf to the Moakley Bridge. Its implementation had been stalled by the often contentious negotiations over zoning for the $1.3 billion tower, which faced opposition first from residents of neighboring Harbor Towers complex and, more recently, from the aquarium. Executives at the popular tourist attraction worried that years of construction work might keep visitors away, further jeopardizing the nonprofit’s already fragile finances.

Eventually, Chiofaro agreed to a plan that would compensate the aquarium for lost business. Along with guaranteeing 250 parking spaces — 500 on nights and weekends — the company will set up a $30 million “indemnification fund” — $10 million in cash, $20 million as a loan — to reimburse the aquarium if visits dip below current levels of 1.37 million per year. Chiofaro Co. agreed to the stipulation, though company officials say they don’t believe lost revenue will come anywhere near $30 million.

They also agreed to direct $10 million toward work on the “Blue Way,” a large open space the aquarium is planning in front of its building on Central Wharf. That’s an increase from $5 million in earlier versions of the plan.

In addition to setting a maximum height and size of the new building, the plan requires that half of the site, which is nearly an acre, be left as open space.

The design of the building itself still is undetermined.

Friday night, Harbor Towers issued a statement that raised questions about the deal.

“We are pleased that the future of the New England Aquarium will apparently be secure,’’ the Harbor Towers statement said. “But this outcome disrespects the state law protecting public access to the waterfront, for the first time ever permitting a 600-foot-tall tower on the Harbor — and less than the 50 percent open space that an important neighborhood group, the Wharf District Council, judged was essential to any redevelopment.’’

Chiofaro said he’s still weighing ideas and will start talking with the city and other interested parties after the harbor plan is approved. Given its spot at the center of the city’s skyline, he said, he wants to make sure it’s a memorable piece of architecture.

“Whatever’s going to be built there is going to be a symbol of Boston forever,” he said. “That’s the opportunity.”

Tim Logan can be reached at [email protected]. Follow him on Twitter at @bytimlogan.