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A slower-than-expected vaccine rollout in the United States may be about to meet a fast-moving new variant of the coronavirus.

Officials in two states, Colorado and California, say they have discovered cases of the more contagious variant, which was first identified in Britain.

A day after Colorado reported the first known case of the variant in the United States, state officials on Wednesday reported a second one. Then later in the day, Gov. Gavin Newsom of California announced that his state, too, had a case in San Diego County.

There is no evidence that the new variant makes people any sicker, but it appears to be much more contagious than older forms. And that threatens to complicate what had seemed a hopeful, if halting, path to recovery from the pandemic in the United States.

The confirmation that the variant, which has upended Britain’s efforts to contain the pandemic, was in the United States came as U.S. officials acknowledged the vaccination drive has been lagging.

Federal health officials said in a news conference on Wednesday that they did not have a clear understanding as to why only a fraction of the doses that had been shipped out around the country have made it into arms.

As of Wednesday, more than 12.4 million doses of the Pfizer and Moderna vaccines had been sent out across the United States, up from 11.4 million on Monday morning. But just 2.8 million people had received their first dose, according to the Centers for Disease Control and Prevention.

“We agree that that number is lower than what we hoped for,” said Moncef Slaoui, scientific adviser of Operation Warp Speed, the federal effort to accelerate vaccine development and rollout. He added: “We know that it should be better, and we’re working hard to make it better.”

The 2.8 million administered doses reported by the C.D.C. is an underestimate of the true number because of lags in reporting. Still, it falls far short of the goal that federal officials put forward as recently as this month to have 20 million people vaccinated by the end of this year.

Gen. Gustave F. Perna, the logistics lead of Operation Warp Speed, said that the C.D.C. was gathering data to better understand the factors driving the slow uptake of vaccines that had been shipped out. “To have greater specificity at this time, after two weeks, I don’t think would be appropriate,” he said.

Still, General Perna pointed to a few possible contributing factors. In addition to the lags in reporting, the holiday season and winter weather have slowed uptake. Hospitals and other facilities administering the vaccines are still learning how to store the doses at very cold temperatures and properly administer them. And states have set aside many doses to be given out to their long-term care facilities, a drive that is just gearing up and expected to take several months.

So far, most vaccines administered have been given out at hospitals, clinics and nursing homes. Dr. Slaoui and General Perna both said they expected the pace of the rollout to accelerate significantly once pharmacies begin offering vaccines in their stores.

The federal government has reached agreements with a number of pharmacy chains — including Costco, Walmart, and CVS — to administer vaccines in their stores and other locations once vaccines become more widely available. So far, 40,000 pharmacy locations have enrolled in that program, General Perna said.

“What we should be looking at is the rate of acceleration over the coming weeks,” Dr. Slaoui said, “and I hope it will be in the right direction.”