Some 5,500 ducks and 500 chickens have died in the last two weeks in two provinces on the Mekong Delta, health ministry officials said.
The government said there was "an extremely high risk" of it spreading widely in the delta region.
Vietnam has been free of human cases of bird flu for a year, following a large culling and vaccination drive.
The last known major outbreak among birds was in December 2005.
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