About 150 ducklings were infected with the virus, leading to the culling of the entire flock of 450 unvaccinated waterfowl in Tra Cu district, Tra Vinh province, the department said in an online report.
Vietnam has now placed four of its 64 provinces and municipalities on its bird flu watchlist, also including Cao Bang near China and the northern mountainous provinces of Thai Nguyen and Dong Thap.
Once the country worst hit by bird flu, Vietnam has controlled the virus with mass culls and vaccination campaigns. But avian influenza came back strongly this year, spreading to 18 provinces and municipalities in May.
This year, four people have been killed by bird flu, bringing the human death toll to 46 since the virus broke out in the country in late 2003.
So far this year, animal health experts have vaccinated more than 163 million head of poultry in an effort to contain H5N1.
The World Health Organisation has recorded 322 cases of bird flu in humans globally, 195 of which were fatal.
Experts fear the virus could mutate and become easily transmissible between humans, leading to a pandemic with the potential to kill millions.