It’s back to the drawing board for the Army Corps of Engineers.

A federal judge Thursday ordered the agency to redo its analysis that approved pile-driving work on a new cruise-ship terminal in downtown Charleston, saying the Army Corps failed to look at all aspects of the project.

The decision by U.S. District Court Judge Richard Gergel adds to the series of delays for the $35 million terminal, which the State Ports Authority has been planning to construct at the north end of Union Pier since 2010.

“I think you did an end run,” Gergel told lawyers representing the Army Corps. “You gave this permit the bum’s rush.”

The Coastal Conservation League and the Preservation Society of Charleston are suing the federal agency over a permit it issued allowing five pilings to be driven on the waterfront for the proposed cruise terminal.

The opponents have said the Army Corps didn’t take into account the impact on historic properties. The pilings are needed to help transform an existing warehouse into the new passenger building. The SPA joined the Army Corps this year in defending its permit.

At Thursday’s hearing, both sides asked Gergel to rule on the issue.

After nearly two hours of oral arguments, he determined the Army Corps granted the permit without looking at such issues as environmental and historical concerns.

“I’m going send this back to you because I feel you did not do a whole review,” Gergel said.

Lawyers for the Army Corps argued that the agency’s jurisdiction was only to review the use of the five pilings. Justice Department Attorney Leslie Marie Hill said the Army Corps does not act as a “super zoning authority.”

Gergel said the agency is responsible for looking at the entire project, citing materials that included designs of the cruise terminal structure and other details.

“You have to put the whole project into the basket for a review, not just five pilings,” he said. Gergel said he it seemed the agency was resistant to analyzing the project in its entirety.

“This makes me think that nobody wants to do it because they’re scared of what the answer is,” he said.

Gergel also noted evidence in the 1,200 pages of court records that the terminal is being designed for larger vessels and could nearly triple the cruise-passenger traffic to call on Charleston. That, in turn, could bring more people and traffic to the historic district.

“This is a serious matter and it needs to be assessed,” he said.

The Army Corps and the SPA released written statements after the ruling, saying they will wait to read Gergel’s formal decision before taking further action.

“We’re now awaiting the judge’s final order, and after review of the order, we will consult with the Corps of Engineers concerning next steps going forward,” according to the SPA. “In the meantime, the Ports Authority will continue to operate our cruise facility in accordance with the voluntary cruise management plan, which has the approval of Mayor (Joe) Riley and City Council.”

Riley said he was confident that the permit “will be approved as it is justified. If the further analysis is required, we are confident that the permit will be supported.”

The voluntary cruise management plan with the city includes capping the number of pleasure-ship calls at 104 a year. The SPA must hold public hearings and other measures if it intends to exceed that limit.

The SPA now uses an aging structure at the south end of Union Pier to handle cruise ships and their passengers.

The dispute over cruises has been raging for several years.

It started to come to a boil 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.

Gergel’s decision was a victory for opponents, who have said the full review of the new terminal has been neglected.

“As we have said all long, this has an enormous impact, and to limit it to just five pilings was not the intent of the law,” said Dana Beach, executive director of the Coastal Conservation League. “We are delighted that the judge affirmed that.”

Beach added that Gergel’s decision could set the tone for a separate lawsuit challenging the S.C. Department of Health and Environmental Control’s permit allowing the pilings.

The Coastal Conservation League, preservationists and some neighborhood associations are asking the state Administrative Law Court to review that approval.

“It’s the same issue. ... The corps and DHEC have narrowed the scope of review to exclude impacts,” Beach said. “They are real in the community and required to be reviewed.”

The SPA recently is asking a judge to dismiss the DHEC case, saying the groups are using the court system to delay the cruise terminal. Beach and other opponents to the project have argued that the courts the proper place to resolve the dispute.

With litigation holding up redevelopment, the SPA has reactivated Union Pier as a cargo port. It’s been handling mostly noncontainerized items, such as paper and metal products.

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