CVS and Walgreens, two of the nation’s biggest pharmacy chains, have tossed out the bulk of their unused COVID-19 vaccine doses and wasted more doses than most states combined, according to a new report. 

The two chains made up about 70% of wasted vaccine doses, Kaiser Health News found, citing government data it obtained. The Centers for Disease Control and Prevention recorded 182,874 wasted doses by late March. CVS made up nearly half of that total while Walgreens accounted for 21%, for a combined 128,500 shots tossed out. 

The KHN survey, published Monday, found that CDC data suggests that Walgreens and CVS tossed out more doses than U.S. states, territories and federal agencies combined. Pfizer’s vaccine, which was the first COVID-19 shot to be approved and had initially required storage at ultracold temperatures, made up almost 60% of wasted doses. 

The raw numbers were obtained through public record requests to the CDC and all 50 states, five major cities, Puerto Rico and the District. But the data has “clear shortcomings,” KHN said, noting that data from multiple jurisdictions are not included in the CDC’s records and that there were inconsistent standards of waste reporting. 

Thirty-three states and D.C. provided KHN some data and reported at least 18,675 more wasted doses across 10 jurisdictions not included in CDC data. Eight more states informed the news agency of wasted doses that had not been reported to the CDC. 

“One thing is clear: Months into the nation’s vaccination drive, the CDC has a limited view of how much vaccine is going to waste, where it’s wasted and who is wasting it, potentially complicating efforts to direct doses to where they are needed most,” KHN said in its report. 

However, no city or state failed to use as many vaccine doses as reported by CVS and Walgreens, the report says. “It’s not completely clear from the CDC data why the two chains wasted so much more vaccine than states and federal agencies,” KHN said. 

Kate Grusich, a public affairs specialist with the CDC, said about 0.13% of more than 310 million total coronavirus vaccine doses were wasted as of Sunday, an “extremely low” rate. 

She said the CDC expects wastage to increase as vaccination supply and opportunities to get the shots expand nationwide.

L.J. Tan, a chief strategy officer for Immunization Action Coalition, said initial problems with vaccine rollout could explain some of the waste. 

“I think that operational issues earlier in the program led to some increased wastage of the more storage-and-handling sensitive doses. But as the temperature requirements began to be understood better, that also gave the retail stores more leeway with the doses and the wastage declined,” he said. 

Walgreens has administered nearly 8 million doses through March 29 and only about 0.5% were discarded due to vaccine mishandling such as broken vials or temperature fluctuations in cold storage, said Erin Loverher, Walgreens corporate spokeswoman.

“As one of the largest vaccine providers in the country, our goal is to use every single available vaccine,” Ms. Loverher said. “Our pharmacists maintain COVID-19 vaccines in a manner that maximizes the shelf life of the products and prevents against loss.” 

To prevent vaccine waste, Walgreens said it worked with long-term care facilities in advance of scheduled clinics to verify anticipated doses based on registrations and also used vaccine doses that were due to expire to inoculate eligible employees according to phased plans by states and federal agencies. 

If there are any excess doses after that, Ms. Loverher said the company communicates with the state and local jurisdictions for vaccine reallocation. 

Matthew Blanchette, CVS Health spokesman, said vaccine waste in its stores is “extremely limited” with less than 0.1% or 1 in 1,000 doses wasted. He said the company has a number of processes in place to reduced waste, including an online scheduling tool that matches appointments to available vaccine supply and outreach to patients if there are any unused doses. 

“We take every precaution to minimize COVID-19 vaccine waste and follow all CDC and manufacturer guidelines with regard to proper storage, transport and administration,” Mr. Blanchette said. 

“Nearly all of our reported waste occurred within the long-term care facility program that began last December due to issues with transportation restrictions, limitations on redirecting unused doses, and other factors.” 

CVS and Walgreens manage about 18,000 of the more than 75,000 vaccination sites in the country and have administered more than 32 million doses nationwide as of Monday, said the CDC’s Ms. Grusich. 

They were also in charge of administering nearly 8 million doses of COVID-19 vaccine to more than 63,000 long-term care facilities nationwide, which involved setting up more than 167,000 onsite vaccine clinics. 

“In these clinic settings, an average of one dose per clinic was reported as wasted. Given these activities and their overall vaccine footprint, their wastage rate is very low,” the CDC’s Ms. Grusich said.Pharmacies overall accounted for almost 75% of wasted doses reported to the CDC while states and some large cities made up about 23% of tossed doses, the KHN survey found. Federal agencies, including the Bureau of Prisons, made up 1.5% while the Virgin Islands accounted for almost 0.2% of wasted doses. 

Although some doses needed to be tossed out, the Immunization Action Coalition’s Mr. Tan said vaccine wastage overall by retail chains and public health entities has been remarkably low. He added that vaccine access should be as open as possible. 

“So let’s say if a retail pharmacy has to open a new vial in order to vaccinate one last person, we would rather that happen, than for that person to not get vaccinated. This is a fine balance that all the providers are trying to balance,” he said.