The strain found in a 20-year-old patient from central Taiwan was of relatively low virulence, but the risk is that it could mix with other viruses to become more dangerous, they said.
"Our report highlights the continuous need for preparedness for a pandemic of unpredictable and complex avian influenza," they warned.
Writing in The Lancet, a team led by Ho-Sheng Wu from Taiwan's Centres for Disease Control (CDC) reported on the case of a woman who was hospitalised in May with a fever, cough and breathing difficulties.
The CDC announced the incident in June. Publication in the peer-reviewed journal provides fuller details of the agency's response and a wider assessment of the risk.
Gene sequencing of a throat swab sample showed that the cause was a local strain of H6N1 influenza virus, the team reported.
H6N1 is a subtype of flu found among wild birds and domestic poultry on many continents.
In Taiwan, though, a unique genetic lineage of H6N1 has evolved over more than 40 years, previous research has found.
The local strain has shown the potential to cross-infect lab mammals, but this was the first time it had been linked to infection in a human.
The sample taken from the woman notably had a so-called G228S mutation in a surface protein called haemagglutinin, helping the virus to latch onto cells in the human upper respiratory tract.
The unnamed woman recovered after being treated with the anti-viral drug Tamiflu, said the study.
When, where and how she became infected with the novel virus is unknown.
Epidemiologists tracked down 36 people who had been in contact with her; six developed fever or a respiratory-tract infection, but none came from H6N1.
The patient worked as a clerk in a delicatessen, had no contact with poultry or raw meat, and had not been abroad for three months prior to infection.
Additionally, no H6N1 virus was found in samples in two poultry farms near her home.
The discovery adds to the list of flu subtypes known to have leapt the species barrier to humans.
At present, epidemiologists are keeping a worried eye on the highly dangerous subtypes H7N9 and H5N1, which can be transmitted from birds to humans.
Transmission is difficult though -- and transmission from human to human is rarer still.
The worry is that the viruses could acquire genes that make them more infectious as well as lethal, developing into a new pathogen against which people have no immunity.
One well-known intermediary for this so-called genetic reassortment is the pig.
It can simultaneously carry avian, human and porcine viruses, thus providing a "kettle" to allow viruses to swap genes.
Three influenza pandemics occurred in the 20th century, killing tens of millions of people. The first flu pandemic of the 21st century occurred in 2009 with the H1N1 subtype, which turned out to have roughly the same lethality as ordinary "seasonal" influenza.
"Our findings suggest that a unique group of H6N1 viruses with the human adaption marker G228S have become endemic and predominant in poultry in Taiwan," said Wu.
"As these viruses continue to evolve and accumulate changes, they increase the potential risk of human infection. Further investigations are needed to clarify the potential threat posed by this emerging virus."