In the commuter ecosystem of New York City, ferry boats have generally been more reliable than other modes of transit and have become an increasingly popular option. So it was an unexpected and alarming development when the longest-running ferry operator in New York Harbor ran afoul of federal regulators over the weekend.

On Sunday, the United States Coast Guard said it had found safety problems with 23 boats in the fleet of 32 run by New York Waterway, the dominant operator of ferries between New Jersey and New York City.

The Coast Guard said the boats were “unfit” for service and ordered that they not be used until the problems were fixed and the boats passed another inspection.

While the Coast Guard said the problems did not represent a safety risk to riders, Waterway was forced to significantly reduce service, causing delays and anxiety for many riders on Monday morning, though by the evening rush the company said it was running close to a normal schedule.