Authorities said there was no reason to believe the deaths were linked to the vaccine but an investigation including post-mortems is underway.
'It makes it hard for us to put out a categorical statement,' vice health minister Kim Gang-lip told a briefing this week about the deaths, which include a 17-year-old boy and a man in his 70s.
Coming just weeks after the rollout of the national vaccine programme was suspended over safety worries, the deaths have dominated headlines in South Korea.
A 17-year-old boy who died on Friday was the first death noted by officials to follow receipt of the vaccine.
The boy died two days after receiving the flu shot in Incheon, near the capital Seoul.
A man in his 70s, who had Parkinson's disease and arrhythmia, was the most recent case. He died in Daegu on Wednesday, a day after receiving the flu vaccine.
Daegu officials said the man had received vaccines since 2015 with no prior adverse reactions.
Officials last month announced plans to procure 20 per cent more flu vaccines for the winter than the previous year.
They hope to inoculate 30million people in a bid to prevent the health system being overloaded by patients with flu and Covid-19 exposure.
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