The World Health Organisation has declared a pandemic is under way from the new H1N1 virus, also known as swine flu.
"This is the first time Tamiflu resistance in HSI virus (was) found in Hong Kong," a spokesman for the health department said in a statement.
Only two other cases of Tamiflu-resistant H1N1 have been found so far, in Denmark and Japan.
According to the statement, the virus was isolated from a specimen taken from a 16-year-old girl coming from San Francisco, who was taken in by the Port Health Office at the Hong Kong International Airport upon arrival on June 11.
The virus was identified during the health department's routine sensitivity test of HSI virus to oseltamivir and zanamivir, the spokesman said.
Tamiflu, a tablet known generically as oseltamivir, is made by Switzerland's Roche AG and Gilead Sciences <GILD.O>, while Relenza, an inhaled drug known generically as zanamivir, is made by GlaxoSmithKline <GSK.L> under licence from Australia's Biota Inc <BTA.AX>.
The department said that tests showed that the strain was sensitive to zanamivir.
Resistance to Tamiflu has been previously documented in the deadly bird flu virus H5N1 and seasonal H1N1 flu.
"You can always expect a certain number of resistances," said Roche spokeswoman Claudia Schmitt. "It does not necessarily mean that the strain is resistant to Tamiflu."
H1N1Ukraine epidemic kills 109
FLU CONTINUES TO SPREADDeath toll rises to 135 in Ukraine flu epidemic
RIGHT TO DIERight-to-die baby 'likes music'
AFGHAN CONVOY ATTACKEDSoldiers, militants killed in southern Afghanistan
FRIENDLY FIRE KILLS SEVEN7 Afghan security forces killed in NATO airstrike
EU BIDCyprus says Kosovo must not hamper Serbia EU bid
AUTONOMYSerbia mulls wide autonomy for northern province
