The infected illegally hatched poultry was found in the provinces of Ca Mau and Bac Lieu in the southern Mekong Delta region, the report said.
Bird flu first arrived in the Mekong Delta in late 2003.
The last outbreak of the virus in Vietnam was detected in August on a small duck farm in the southern province of Ben Tre, also in the Mekong Delta.
H5N1 has evolved into a virus that inflects more species than any previously known flu strain.
Health experts fear it could mutate into a form that becomes easily passed among people, potentially sparking a pandemic, although so far, most human cases have been traced to contact with infected birds.
Since it first emerged the virus has killed 93 people in Vietnam, more than it has killed in any country.
Other countries which have reported human cases of the disease include Cambodia, China, Indonesia, Thailand, and Turkey.
Vietnamese officials say the new outbreak is especially worrying because it coincides with cooling temperatures in the Mekong Delta region, conditions in which the virus thrives best.