Ion Agafitei, the chief veterinarian, told reporters on Saturday that three birds had tested positive for the virus in the village of Smardan.
The country reported its first cases of the disease, a strain of which can be dangerous to humans, on Friday.
"We have killed 220 [domestic] birds so far in Ceamurlia de Jos, where the first cases occurred," Agafitei said. "The process is ongoing and will continue."
He said further tests would be undertaken to discover if the virus was harmful to humans. Quarantines had been imposed on other six villages where suspect bird deaths occurred in recent days.
The H5N1 avian flu virus has infected more than 100 people, killing at least 60 in Asia since late 2003, and has decimated flocks of poultry in Southeast Asia.
H5N1 has been officially registered in six Russian regions in Siberia and the Urals, and has also been confirmed in Kazakhstan.
The Danube delta contains Europe's largest wetlands and is a major migratory area for wild birds coming from Russia, Scandinavia, Poland and Germany.