The A/H1N1 virus killed a three-year-old girl and a 51-year-old man in Göttingen, a Health Ministry spokesman in Hannover said.
“These tragic cases show that this influenza isn't just a harmless illness, and that it can take a turn for the worst,” Lower Saxony's Health Minister Aygül Özkan.
State health official Dr. Matthias Pulz said there had been a marked increase in infections in Lower Saxony since last month.
Özkan warned there was no reason to panic. But she urged people over 60, pregnant women and those with chronic illnesses to get themselves vaccinated for swine flu.
An estimated 250 people have died from swine flu in Germany since the virus emerged in 2009.