"We are filling the stockpile in anticipation of a possible problem in the fall. We are doing everything we can beneath the surface, working as hard as we possibly can," Navarro told CNN's Jake Tapper on "State of the Union."
Asked by Tapper if the administration is preparing for a second wave in the fall, Navarro replied, "Of course."
"You prepare for what can possibly happen. I'm not saying it's going to happen, but of course you prepare," he added.
CNN has reached out to the White House for comment.
Navarro's comments come as Vice President Mike Pence, who's leading the Trump administration's coronavirus task force, has downplayed the threat of a second wave that public health experts are warning about.
In a Wall Street Journal op-ed last week, Pence blamed the media for inciting "panic" regarding a second wave of coronavirus.
"In recent days, the media has taken to sounding the alarm bells over a 'second wave' of coronavirus infections. Such panic is overblown," he wrote.
President Donald Trump was criticized for downplaying the virus's threat and severity at the beginning of the outbreak and his administration struggled to get medical supplies to frontline workers and distribute testing kits.
During a campaign rally in Tulsa, Oklahoma, on Saturday, Trump said he told officials in his administration to slow down coronavirus testing because of the rising number of cases in America.
"When you do testing to that extent, you're going to find more people; you're going to find more cases. So I said to my people, 'Slow the testing down please,'" Trump said in comments that drew immediate criticism from Democrats.
Nearly 120,000 people have died in the US from the coronavirus and medical experts say that testing is critical to identifying and tracing Covid-19 cases and slowing the spread of the virus.
Navarro told Tapper on Sunday that the President's comment was "tongue in cheek" and a "light moment for him at a rally."
Tapper pushed back, saying, "I don't know that it was tongue in cheek at all" and that Trump "has said similar things for months."
Some states, like Florida, Arizona, Texas and North Carolina, have seen an increase recently in positive coronavirus cases. The administration and state leaders say the rise in cases is due to more testing availability. But epidemiologists argue case numbers should go down with greater testing, because theoretically health officials should be able to trace the cases and slow the spread of the virus.
Dr. Anthony Fauci, the nation's top infectious disease expert, told The Washington Post on Thursday that the US is still "in the first wave" of coronavirus.
Fauci previously told CNN that it’s “not inevitable” that the US have a “second wave” in the fall “if you approach it in the proper way,” advising that Americans continue to follow social- distancing recommendations and wear masks in public.