RSPB Scotland said the highly pathogenic avian influenza (HPAI) may also have accounted for the deaths of chicks from at least four white-tailed eagle nests on the Inner Hebridean island in recent weeks.
Inspections of the nests found the birds – also known as sea eagles – had died shortly before or after fledging.
Dave Sexton, RSPB Scotland’s Mull Officer, described the spate of chicks' deaths as "heart-breaking".
In mid-July, a total of 19 white-tailed eagle chicks were on the verge of fledging from nests on Mull, which would have been just one fewer than the record number in 2021.
Mr Sexton, who monitors the huge birds, said that around that time he started receiving reports of suspected dead chicks from multiple locations.
RSPB Scotland and NatureScot arranged for expert climbers to scale Sitka spruce trees to access two of the nests to swab carcasses for HPAI. The remains at two of the other nests were too decomposed to be tested.
Climbers wearing full PPE found both chicks dead in the 12 metres high nests. The swab taken from the most recently deceased chick tested positive for HPAI. The other was negative, although the advanced state of decomposition may have affected the results.
The deaths have made a significant contribution to a large drop in white-tailed eagle breeding success on Mull this year.
White-tailed eagle chicks always have challenges to overcome during their first few months and this year bad weather in the spring and tree collapses have already had an impact on survival rates.
Now, just half as many chicks on the island are expected to survive compared with 2021.
However, one chick hatched this summer to the UK's oldest and most famous white-tailed eagles, the Mull pair known to millions of nature lovers as Skye and Frisa, appears to be thriving.
Mr sexton added: "These past few weeks though have instead been heart-breaking with so many chicks dying. Visiting nest after nest where, instead of hearing young birds calling, there’s silence, and where adult birds are ignoring my presence rather than alarming, is awful.
"such a substantial loss of this year’s youngsters is very worrying.
"My one uplifting moment in all this has been finding Skye and Frisa’s 25th chick alive and well and flying confidently. I can only hope that she survives and that adult birds on Mull continue to be unaffected."
The chick confirmed with avian flu joins thousands of wild birds that have already died in the UK because of the unprecedented HPAI outbreak.
The outbreak appears to have had the most serious impact on seabirds including great skuas and gannets. The first Scottish white-tailed eagle thought to have been killed by avian flu was found dead on Skye November 2021.
White-tailed eagles are the UK’s largest bird of prey with an 8ft wingspan and the species being nicknamed "flying barn doors".Hunted to extinction in Scotland by 1918, when the last native bird was shot on Shetland, they were reintroduced to Scotland on the Isle of Rum in 1975, with further releases in Wester Ross and in Fife.