New York City’s seemingly star-crossed bike-share program, once promised for last summer but delayed until the spring amid software problems, has found its way into Hurricane Sandy’s unsparing path.

The storm dumped several feet of water at some points across the Brooklyn Navy Yard, where the city had been storing equipment like bicycles and docking stations in Building 293, near the northern tip of the yard and the waters of Wallabout Bay.

Building 293 was among those that flooded, and a spokesman for the mayor’s office said Tuesday that there appeared to be damage to program equipment, including docking stations for bicycles, as a result.

“We’re working on it,” Janette Sadik-Khan, the city’s transportation commissioner, said when reached by telephone on Tuesday afternoon. “We had six feet of water in the Brooklyn Navy Yard.”

Officials said it was premature to estimate whether the flooding could affect the program’s start date, scheduled for next March.

The city’s Transportation Department would not describe or detail the extent of the damage; officials released a brief statement on Tuesday saying the agency was “making an assessment” and would provide updates if the program’s rollout might be affected.

The docking stations would appear to be particularly vulnerable to any flooding, given their electronic components, though officials did not respond to questions about potential damage.

The Brooklyn Navy Yard declined to comment on the bike equipment specifically, but said some of the 275 businesses at the yard “suffered significant losses to machinery, equipment and inventory.”

Asked about the financial and insurance ramifications of any damage to equipment, Julie Wood, a spokeswoman for Mayor Michael R. Bloomberg, noted, “We don’t own the bikes.”

Alta Bicycle Share, the company operating the bike-share program, referred questions to the Transportation Department.

On Wednesday, inside Building 293, there was little outward sign of flooding, though heaps of cardboard, which appeared damp and stained, were piled near the thousands of bikes being kept indoors. A man, who would not give his full name as he helped to move some of the bikes, was asked if there had been flooding.

“Yes,” he said quickly, returning to his work.

Since the introduction of the program, seen as a likely centerpiece of the Bloomberg administration’s transportation legacy, officials have often been fiercely protective of details and developments — from the process of selecting an operator and sponsors, to the reasons for the program’s delay last summer.

Any further setbacks would surely frustrate city riders. Many had noted, as transit options dwindled in the immediate aftermath of the hurricane, that bike sharing was already sorely missed.

“New Yorkers have been patient,” Paul Steely White, the executive director of Transportation Alternatives, said in a telephone interview on Tuesday. “I think that with any more delays, New Yorkers’ patience will start to wear a bit thin.”

He included himself in that group.

The program was initially scheduled to begin a partial rollout last summer, then expand to a total of 10,000 bikes and 600 stations by summer 2013. In August, the city announced that the program would begin with 7,000 bikes at 420 stations in March 2013.

“The software doesn’t work,” Mr. Bloomberg said at the time, explaining the delay. “Duh.”

Ms. Sadik-Khan said in August that the city, which became aware of the software issues last spring, did not initially anticipate that the operating code would need to be written “from scratch” — the result of a dispute between Public Bike System Company, Alta’s partner based in Montreal, and 8D Technologies, which had supplied the software for successful programs in cities like Boston and Washington.

But a spring start date, Ms. Sadik-Khan said in August, allowed the city “more than enough time to work out the remaining issues.”

Annie Correal contributed reporting.