Tests have confirmed the H5N1 virus infected waterfowl in three northern provinces of Son La, Quang Ninh, Nam Dinh and the southern Mekong delta city of Can Tho from May 16 to May 19, the Agriculture Ministry's Animal Health Department said.
The dead ducks were found on seven farms which were raising a combined 5,850 ducks. None of them had been vaccinated against bird flu, the department said in a daily report on the disease.
"All the infected poultry stocks in the provinces have been slaughtered, the areas disinfected and protective vaccination was taken," it said. More ducks died in a district in the central province of Nghe An, state-run Voice of Vietnam radio said.
The H5N1 virus has killed 42 people in the Southeast Asian country since it re-surfaced in Asia in late 2003 but Vietnam has had no human cases since November 2005.
The virus returned to poultry in the south late last year and earlier this year.
Apart from killing birds that have not been vaccinated, the spread of the virus in May at the beginning of summer is unusual as experts have previously said it thrives best in cool temperatures and weakens in warmer weather.
Last month the World Health Organisation urged Vietnam to accelerate poultry vaccination and target more ducks.
Vietnam has so far this year vaccinated 116.6 million poultry in 60 out of its 64 provinces.