“The virus has been identified in three ducks in the village of Ceanurlia de Jos,” Agriculture Minister Gheorghe Flutur said.
“We have already imposed quarantine measures in the village and the health authorities in the Danube delta have been put on alert,” he said.
Authorities have ordered that all farm birds in the region must be kept indoors.
Test results showing the dead ducks to be H5N1 positive have been sent to London for further investigation.
It is believed they contracted the virus from migrating birds from Russia.
Authorities have sealed off the village and banned hunting and fishing in eight counties in the region.
Romania has also halted chicken and poultry imports from 15 countries, mostly Asia.
While there have been no reports of sickness in the village, Health Minister Eugen Nicolaescu said the government will step up its anti-flu vaccination campaign for residents of the Danube delta, a haunt of migrating birds.
Romanian authorities took steps last month to start vaccinating all birds in the delta in a bid to prevent a spread of bird flu.
A strain of bird flu known as H5N1 has killed 63 people in Southeast Asia since 2003, most of them in Vietnam.
The World Health Organisation fears the virus might mutate into a human strain, potentially causing a global health pandemic.
Top health officials from 80 countries are taking part in a summit in Washington on how to best respond to such a health crisis.
US researchers have warned the US is woefully underprepared for such an outbreak.
“The highest possible threat (we face) is avian flu,” said epidemiologist Jeffrey Duchin, speaking to an Infectious Diseases Society meeting in San Francisco.
“You know the storm is brewing, it’s about to hit us, we need to prepare, we have time, there’s no excuse,” he said.
This comes as US President George W Bush met with the heads of major pharmaceutical companies to urge them to speed up work towards a vaccine.
Officials participating in the bird flu session say the US hopes it will produce 10 to 15 key priorities for countries to implement, including transparency of quick and accurate reporting of outbreaks, donor support for affected countries and a pledge to work with the WHO.