South Carolina regulators issued the final permit the State Ports Authority needs for its new cruise terminal in downtown Charleston, and the terms include capping the number of pleasure-ship calls at 104 a year.

But the project remains docked by litigation seeking to halt it.

The permit from the state Department of Health and Environmental Control included a voluntary agreement between the SPA and city of Charleston that limits like the size of cruise ships and the number of annual cruise stops.

The SPA wants to relocate its cruise passenger building to a warehouse at the north end of Union Pier, near Laurens Street. The existing structure is farther south, near the end of Market Street.

Several downtown neighborhood associations, environmental groups and preservationists have opposed the new site and have called for limits on cruise operations. Lawsuits have been filed, including one pending before the state Supreme Court.

On Tuesday, some of the opponents applauded the voluntary limits, but said the permit fell short of addressing all of their concerns.

“It was important enough to include the condition in the permit and therefore they have affirmed the material significance in that agreement,” said Dana Beach, executive director of the Charleston-based Coastal Conservation League.

Beach said the permit should have included that cruise ships run offshore-based power on sources rather than their engines to reduce air pollution.

News of the permit approval came during the SPA’s monthly board meeting Tuesday afternoon. The issue was not discussed, but the port released a statement shortly afterward, saying the permit was the last authorization it needed to move forward with construction.

“This is another positive step toward advancing Charleston’s new passenger terminal, which will provide numerous benefits to the community while more effectively supporting our port’s cruise business,” according to the statement.

It went on to say that the terminal plan was a result of “100 meetings with community and stakeholder groups as well as the approval of the city’s Board of Architectural Review.”

Jim Newsome, the ports authority’s CEO, was not available for additional comment Tuesday.

The dispute over cruises has been raging for several years. It heated up in 2010 when Carnival Cruise Lines permanently based its 2,056-passenger liner Fantasy at Union Pier, giving the city a year-round pleasure-ship industry for the first time.

Previously, a handful of seasonal cruises originated in Charleston.

Opponents have said the new terminal will bring more tourists, traffic congestion and fumes to the historic district. They also have raised quality-of-life concerns about the ships disturbing nearby residents with their horns and passenger announcements.

Preservation Society Executive Director Evan Thompson said the proposed terminal still will put the historic neighborhoods at risk.

“While our port is old, our modern mega-cruise-ship industry is new, and it must be properly located and managed responsibly within an enforceable legal framework,” he said Tuesday. “We are disappointed that the permit for this new terminal has been issued without taking into consideration the feasibility of alternative sites that would mitigate the negative land-based impacts of this expanded and intensified cruise ship operation.”

Supporters such as the Maritime Association of South Carolina disagreed, saying the new terminal will have a positive impact on the port and the region.

“It’s time for port opponents to end all their legal maneuvering and allow this worthwhile project to move forward,” Pam Zaresk, the group’s president, said in a written statement. “The SPA has gone above and beyond what is required during this process and has proven that arguments against the new cruise terminal are unfounded.”

The DHEC permit allows the SPA to install five pilings under Union Pier on the Cooper River to support elevators and escalators. The port plans to convert an existing warehouse into its new passenger terminal.

“We all have our personal beliefs and perceptions about what we wish were the case,” said Catherine Templeton, DHEC’s executive director. “But at the end of the day, our commitment is to look at what the law requires. And at the end of the day, five pilings do not allow more ships or bigger ships.”

Also, the site in question has been an industrial and commercial area for centuries, and “putting in the five pilings doesn’t permit more,” she added.

The SPA and opponents have 15 days to appeal the state permit. Beach of the Coastal Conservation League said his group has not decided whether it will.

The cruise terminal is tied up by litigation, including a federal lawsuit that seeks to force the Army Corps of Engineers to revisit its decision to issue a federal permit for the project.

Reach Tyrone Richardson at 843-937-5550 and follow him on Twitter @tyrichardsonPC

he Associated Press contributed to this story.