Officials initially said the unnamed man died on July 10 from methicillin-resistant Staphylococcus aureus (MRSA), a virulent bacteria that has emerged as a major health threat in hospitals around the world.
But officials said they found from test results Thursday that the cargo ship crew member was also suffering from A(H1N1) influenza, also known as swine flu.
"He had two infections at the same time," Thomas Tsang, controller of the government's Centre for Health Protection, told reporters.
"At this point in time, we cannot rule out that human swine flu may have played a part in his death," he said.
He added it was very likely that the deceased was infected with the flu outside Hong Kong.
The seaman arrived in Hong Kong from the Philippines to work on the ship on June 28. He developed symptoms including cough and fever on July 3, after the ship left Hong Kong waters.
The Filipino was immediately admitted to hospital after he returned to Hong Kong, and was diagnosed with pneumonia and respiratory failure before passing away.
Tsang said the vessel arrived in mainland China with about 20 crew members mostly from the Philippines and Greece. Officials are checking with the Beijing government to track them down, he added.
A total of 1,552 cases of swine flu had been reported in Hong Kong by Thursday afternoon, the health official said.
Excluding the seaman's case, five have been classified as serious and are in hospital.
Tsang said summer is the peak flu season and he expected that the case numbers would continue to climb and the city could have its first fatal case any time.
When Hong Kong discovered its first swine flu case in early May, health authorities quarantined around 300 guests and staff at a hotel where the carrier, a Mexican national, had briefly stayed.
In June, authorities ordered all primary schools in the city to be closed for two weeks after the first cluster of local swine flu cases was found.