Singer and guitarist Ku Ku performs behind the Torpedo Factory Art Center in Alexandria in June 2011. Alexandria’s Board of Zoning Appeals voted to halt Plans to redevelop the waterfront area early Friday. (Tracy A. Woodward/THE WASHINGTON POST)

The future of Alexandria’s waterfront was thrown into question early Friday when the Board of Zoning Appeals ruled that city officials wrongly denied a protest petition on the issue.

The city said later Friday that the ruling could affect the zoning of several parcels on the waterfront but that it does not overturn the City Council’s Jan. 21 approval of the waterfront plan. The City Council will meet in closed session Saturday with city attorney Jim Banks and City Manager Rashad Young to evaluate their options.

“The waterfront plan, which was approved by a majority of the City Council, is officially part of the city’s master plan,” Mayor William D. Euille (D) said. “The BZA decision on the protest petition will not halt the plan’s implementation; however, ensuring a change in zoning use is a critical element of the plan.”

Banks had said shortly after the 1 a.m. vote that the city would appeal the board’s decision to Circuit Court. Later Friday, he said that the board’s decision “did not fully address the legal issues brought before them” and that he would present the legal options to the council members.

The petition, had it been accepted in January, would have forced the City Council to pass the waterfront plan by a “super-majority” vote. The council passed the plan 5-2, one vote short of super-majority.

Andrew Macdonald, one of the leaders of the residents group that has fought Alexandria over the issue and who is an independent candidate for mayor, said he had hoped the zoning board’s decision would prompt the city to work with his organization. After hearing the city’s response, he said: “I don’t think the city has any intention of . . . sitting down with the community and working to revise the plan.”

The controversy over how to redevelop Alexandria’s waterfront has gone on for a year, and residents are divided over whether it is a good plan. Opponents say that it will bring too much density to the area and that city staff members listened more closely to developers and corporations than to residents.

The city says it spent two years soliciting public comments and made numerous alterations to the plan based on the response. Two of the properties whose uses are in dispute are owned by Robinson Terminal Warehouse Co., a subsidiary of The Washington Post Co.

The zoning board got involved in the dispute because Faroll Hamer, the city’s planning director, refused to accept the petitions both the day before and the day of the council’s Jan. 21 vote. She said that the petition was allowed only when a zoning map was changed and that the waterfront plan was a change in the zoning law text.

Opponents pointed to a line in the rules that said either map or text amendments could be challenged, but city officials said opponents were misreading the rule.

Board of Zoning Appeals members said that although their decision was a close call, Hamer’s basis for refusing the petition was wrong. Board Chairman Mark Allen recused himself because as a lawyer, he represents a waterfront property owner.