Researchers say it is unclear how the man contacted the virus, but refuse bins outside his home were infested with rats.
There had been no previous evidence that this strain of the virus could be transmitted to humans.
The human version of hepatitis E is usually spread through contaminated drinking water.
Doctors discovered the case when tests on the man showed abnormal liver function following a liver transplant.
Further tests showed that he was carrying a strain of hepatitis "highly divergent" from the strain that affects humans, researchers from the University of Hong Kong said.
"We postulate that contamination of food by infected rat droppings in the food supply is possible," they said in a report.
The man is said to be recovering.
Symptoms of the human strain of hepatitis E include jaundice and sometimes tiredness, fever, nausea, vomiting and abdominal pain.
Most people will get over the virus, although for some, such as those with an immune deficiency disorder or pregnant women, it can prove fatal.
It is common for diseases to spread from animals to humans. More than 60% of emerging infectious diseases originate in animals.
A sustained period of hot and humid weather has caused rodent problems in Hong Kong to escalate.
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