There was no indication the three contracted the disease from each other and no signs of H7N9 infection among the 88 people who had closest contact with them, the medical agency said.
However, two relatives of the 87-year-old victim developed pneumonia around the same time he did. Their diagnoses have yet to be confirmed. One of them - his 55-year-old son - has died.
University of Hong Kong's Centre of Infection president Dr Ho Pak-leung said H7N9 infections seen in poultry were usually mild. "This time it has caused deaths and critical conditions, even in young patients. This shows that there is a chance of virus mutation," he said.
But Guangdong Health Department spokesman Feng Shaomin said the department saw no need to launch emergency measures among tourists ahead of the Ching Ming Festival.
Influenza diagnosis tests in Hong Kong target the more common swine influenza and the H5N1 avian influenza. Ho said H7 viruses were less common in Asia and adjustments to the tests may now be needed.
H7N9 is a statutorily notifiable infectious disease in Hong Kong.
There is no vaccine. Some Shanghai residents and internet users were angered at the delay in disclosing the three cases. But Ho said the delay was understandable as time was needed to identify the virus.
Hong Kong's Centre for Health Protection said it was maintaining close contact with mainland health authorities and reminded the public to observe personal hygiene.