The planning for a crucial swath of Boston’s waterfront — 42 acres stretching from Long Wharf to the Northern Avenue Bridge — began in 2013.

It only seems longer than that.

So it’s not exactly a shocker to find out that the process, which was set to wrap up this fall, will stretch on for at least a few more months. The main obstacle to a resolution: an ongoing squabble between New England Aquarium and developer Don Chiofaro over details of a skyscraper Chiofaro wants to build on the site of the Boston Harbor Garage.

State officials have extended into late November their review of zoning for the area, which initially was set to wrap up Aug. 21. That means final approval probably won’t come until December.

The move to put off a decision on zoning is only the latest delay. The goal is to rezone 42 acres along the waterfront, a process that has been dominated throughout by debate over Chiofaro’s skyscraper, which would be among the tallest in Boston and could transform a key part of the waterfront.

In March, the Boston Planning & Development Agency approved rules that would allow for a 600-foot-high tower on the site, while also opening up more space on the street than the current blocky garage allows. But as the plan moved toward state approval, talks bogged down again, this time over whether Chiofaro will reimburse the aquarium, which is next door, for lost business during construction.

The nonprofit derives most of its roughly $50 million in annual revenue from visitors, many of whom drive to the aquarium, and sometimes use the Harbor Garage for parking, said aquarium executive vice president Eric Krauss. Turning that garage into a massive construction site for three or four years could pose an “existential’’ threat to the aquarium, Krauss has said. Aquarium officials are pushing Chiofaro to agree to cover any financial losses.

“We’re not looking for the ­Chiofaro Co. to write a big check up front, but we do need assurances that we’re covered,’’ Krauss said. “We don’t have that big of a net.’’

Citing confidentiality agreements, neither side would discuss specific terms, but Chiofaro agreed the revenue guarantees were the biggest sticking point. He said he was optimistic that they’d reach a deal soon, and that, in the end, his project will only bring more people to the aquarium’s front door — especially if both sides can work together to create the so-called Blue Way the aquarium proposed in the Central Wharf area last year. It would include park area as long as 1,000 feet and up to 85 feet wide that would extend from the site of Chiofaro’s tower, along the Rose Fitzgerald Kennedy Greenway, to the harbor’s edge.

“We want to go from being ‘an existential threat’ to the aquarium to being the biggest patron they’ve ever had,’’ Chiofaro said. “I am very optimistic that we’re going to get to ‘yes.’ ’’

Other neighbors, including some residents of nearby Harbor Towers complex, also have criticized Chiofaro’s plans, raising concerns that the project will set a dangerous precedent for building along the waterfront. But the aquarium has extra leverage ­under state laws that protect ­water-dependent institutions from development along Boston Harbor, and city officials have said they won’t OK any plan that puts the nonprofit at financial risk.

It was the BPDA that requested the zoning decision extension. Rich McGuinness, who leads waterfront planning for the agency, said in an e-mail that he hoped the extra time would enable more comprehensive planning.

“Public benefits are a key ­component of this planning ­process, and the BPDA is focused on shaping high quality public realm improvements, including the concept of the Blue Way that was proposed last year,’’ McGuinness wrote. “We are working with the state on structuring the [plan] to make it a possibility.’’

A spokesman for the state environmental agency that is reviewing the plan said officials hope to balance development with open space, public access, and water-based institutions like the aquarium.

Even once the rezoning is complete, Chiofaro has a long road ahead before he can start construction. He’ll still need to seek both city and state permits for his tower, a process that often takes months, if not longer. After more than a decade working on the project, Chiofaro said, he’s eager to get going.

“We can build a great building there,’’ he said.

Some observers welcomed the extra time, saying they hoped this latest pause will give the state a chance to take a broader view of the plan — and waterfront development in general — rather than focusing narrowly on the long-contested garage site.

“Our hope is that this extension signals that we’re moving toward a plan that is more holistic in how it approaches the waterfront,’’ said Jill Valdes Horwood, policy ­director for the advocacy group Boston Harbor Now. “While the individual parcels are important, it’s not enough to speak parcel by parcel. We really need a more ­cohesive vision for the waterfront.’’

Tim Logan can be reached at tim.logan@globe.com. Follow him on Twitter at @bytimlogan.