However it is not yet clear whether the virus detected is the strain deadly to humans.
Earlier, EU veterinary experts said there was no avian influenza in Romania, but would remain on alert for the deadly virus after an outbreak in Turkey.
The commission said it plans to ban imports of live birds and poultry products from the east European country following the findings, which contradict the other test results.
“The three EU laboratory experts sent to Romania by the Commission last Monday have confirmed that avian influenza virus H5 has been detected in tests on two samples from a chicken and a duck taken in a suspected backyard farm in the Danube delta,” the EU commission said in a statement.
Suspected cases of avian flu in Romania and an outbreak in Turkey rang alarm bells in the EU.
Chief veterinarian Ion Agafitei said scientists detected the H5 virus in samples taken from three ducks.
Ban on Turkish poultry
The commission also confirmed the bloc would extend its ban on poultry products and pet birds from Turkey until April 2006.
Full results of tests for the exact strain of bird flu detected in Turkey are due on Friday.
Turkish officials said they had completed a mass slaughter of birds to combat an outbreak in the northwest of the country, although the area remained quarantined.
While avian influenza affects birds, one strain of the virus known as H5N1 has killed more than 60 people in South East Asia since 2003.
Scientists have warned that millions of people worldwide could die if the H5N1 strain crosses with human flu strains to become highly contagious among people.
Samples from infected animals in the area around the Turkish village of Kiziksa have tested positive for the H5 virus, but it was not yet known whether it was the H5N1 strain.
Germany tightens imports
Germany meanwhile plans to tighten controls at all points where imported poultry enters its borders in a bid to avoid a bird flu outbreak.
“The biggest risk is posed by the illegal importation of poultry and food,” the secretary of state for the consumer ministry, Alexander Mueller, said.
He said special attention would be paid to poultry coming from Asia and Turkey.
Experts have decided against drastic measures like quarantining poultry farms or ordering the mass slaughter of birds.
Mr Mueller said tests carried out on poultry and migrating birds in Germany have so far revealed no trace of the disease.
Australia bolsters defences
Australia will spend A$10 million helping Indonesia bolster its defences against bird flu.
A team of Australian experts visited Jakarta last week to assess how well the country could cope with the disease.
So far bird flu has officially claimed three lives in Indonesia.
Australia has already provided Indonesia funding for 50,000 doses of anti-viral medication to combat bird flu.