In a statement, it said a man, 76, who had taken both Sinovac doses, died of pneumonia on Monday.
The man, who had suffered from hypertension, diabetes and hyperlipidemia, was admitted to Tseung Kwan O Hospital on April 5, five days after he had received his second Sinovac jab. He was diagnosed with hypertensive intracranial haemorrhage.
A woman, 74, died on Sunday also of pneumonia, having taken both doses of the BioNTech vaccine.
The woman, who had suffered from pulmonary fibrosis, was admitted to Eastern Hospital with breathing difficulties, about two weeks after she got her second BioNTech shot on April 7.
The Health Department said an expert panel will look into the cases and there is no indication so far that the jabs were responsible for the deaths.
It added that, as of Sunday, 15 deaths had been reported within 14 days of vaccination, which accounted for 0.001 percent of 1.3 million doses of Covid vaccines administered in Hong Kong.
The expert panel has concluded that three of the 15 deaths had no causal relationship with the jabs, and considered that eight cases were not related to the vaccination according to its preliminary analysis. The remaining four cases are yet to be assessed.