President Joe Biden's Chief of Staff Ron Klain said there was no plan in the federal government for the distribution of vaccines across the US.
The president, who took office last Wednesday, has promised 100 million vaccine shots in his first 100 days.
The US has now reported more than 25 million Covid-19 cases.
About 417,500 deaths have been linked to the virus. In recent weeks, the daily number of Covid-linked deaths in the US has, on some days, exceeded 4,000.
President Biden signed a raft of new measures last week, including boosting vaccinations and testing. He has implored Americans to wear masks and warned that the death toll could get much worse.
"Let me be clear - things will continue to get worse before they get better", he said.
President Biden's efforts follow widespread criticism of the Trump administration's handling of the pandemic and of the vaccination programme.
Vaccines have been distributed to states, and states and cities are carrying out the inoculations. But some have complained they are struggling with supply.
According to the US Centers for Disease and Control, about 41 million doses had been distributed by Saturday across the country, but only 20.5 million had been administered.
Speaking to NBC News, Mr Klain said: "The process to distribute the vaccine, particularly outside of nursing homes and hospitals out into the community as a whole, did not really exist when we came into the White House."
He said it was a "complex" process but that the Biden administration would set up federal vaccination sites to help states without enough places.
How bad is the situation across the US?
Total cases went over 25 million on Sunday, according to tracking data from Johns Hopkins University.
Infections have spiralled in recent months - with a jump in new infections after Thanksgiving and Christmas, according to the Covid Tracking Project.
Hospital numbers hit their highest levels during the pandemic earlier this month but are slowly starting to drop alongside daily cases.
Dr Anthony Fauci, the top US infectious disease expert, said on Thursday that rolling average data appeared to show infections levelling off.
Although the national picture has stabilised slightly, he warned the country remained in a "very serious situation".
The CDC is particularly concerned that new variants could accelerate the virus spread. It issued a warning that the new more transmissible strain first detected in the UK could become the dominant strain across the US by March.
The strain has been detected in 20 states, Dr Fauci said Thursday, but warned the country had "limited ability" to track its spread through the population.
What is being done to combat the virus?
President Biden has already enacted a raft of executive measures to combat the virus and he wants Congress to pass a $1.9tn (£1.4tn) package of economic relief funding.
The president is hoping to get bipartisan approval for his broad stimulus agenda, but the proposal has already been met with scepticism and resistance by some Republicans.
Another one of the new president's key promises is to oversee 100 million vaccinations in his first 100 days in office, but some have criticised this policy as not ambitious enough.
"When I announced it, you all said it's not possible," Mr Biden said on Thursday when asked if his goal was high enough. "Come on, give me a break, man. It's a good start."
The current approved suppliers - Moderna and Pfizer - have pledged to deliver 200 million doses by March. Dr Fauci has also suggested emergency approval of a third vaccine, a single-dose jab by Johnson & Johnson, could be just weeks away.
Dr Fauci, who was appointed chief medical adviser by the new president, has expressed hope that if 70-85% of the US population is vaccinated by the end of summer, the country could "approach a degree of normality" by autumn.
"It's not going to be perfectly normal, but one that I think will take a lot of pressure off the American public," he told a White House briefing.
President Biden's administration has also re-engaged with the World Health Organization (WHO) and is joining its Covax programme to help ensure vaccine access worldwide. The move was welcomed by WHO chief Dr Tedros Adhanom Ghebreyesus.
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