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.
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 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.
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