Just 22 of the 69 pups born last year are still alive, said Doug Smith, the park's wolf project leader. That's the biggest drop in pup numbers since wolves were reintroduced to the park 11 years ago.
The greatest toll was seen on the park's northern range, where only eight of the 49 pups born last spring survived.
"It's cause for concern, a great deal of concern," Smith said.
During the next few weeks, he said, officials plan to catch Yellowstone wolf pups and take blood samples to see if his suspicions about the disease, parvo virus, are true. The disease can cause extreme diarrhea and dehydration and kill more vulnerable animals, like young pups.
Though vaccinations are an option — many domestic dogs receive them — Smith said it would be difficult in the park.
"It requires two vaccinations to build up an immunity, and we'd have to catch every wolf," he said. "Both those things are impractical."
If parvo virus is confirmed, there is little officials can do besides monitor the population and hope exposed wolves build a natural immunity to the disease, he said.
The state's wolf program leader also suspects parvo virus is behind the deaths.
Carolyn Sim said her suspicions are based on den-site monitoring and whether pups emerge in summer with their packs.
State wildlife officials plan to collect blood from wolves — possibly even from carcasses dead 24 hours or less — as part of their disease surveillance, she said.
Terry Kreeger, supervisor of veterinary services for the Wyoming Game and Fish Department, said that while parvo virus could have a noticeable effect for years on wolf populations like Yellowstone's, he doesn't believe it will be devastating.
It could, however, have implications for how wolves are managed, Smith said. The number of wolves in Yellowstone dropped last year from 171 to 118, he said. The largest single-year drop before that was 11 from 1998-99, when parvo virus also was suspected, he said.
The gray wolf is federally protected, but Wyoming officials are seeking more control over the predators amid complaints from farmers and ranchers who say the growing wolf population poses a threat to wildlife, livestock and pets.
Montana recently took over most management duties within its borders, and Idaho signed an agreement with the Interior Department on Thursday to do the same.