A European Union laboratory in Britain was to provide final, official confirmation later in the week, but Reinhard Kurth, president of the Robert Koch Institute, said officials were already taking measures to prevent the disease from spreading.
Chancellor Angela Merkel's Cabinet was discussing further possible measures in addition to ordering farmers to keep all poultry and domestic birds indoors.
In other developments:
Bird flu has killed at least 91 people since 2003, according to the World Health Organization. Almost all the human deaths have been linked to contact with infected poultry, but experts fear the H5N1 virus could mutate into a form that spreads easily among people, possibly sparking a pandemic.
The swans were found Tuesday on a beach on the Baltic Sea island of Ruegen and a preliminary test indicated they carried H5N1. German experts have since conducted a series of other tests, all of which came out positive. A crisis team has been set up in the region.
"Unfortunately these swans were infected with H5N1 from Asia," Kurth told ZDF television. "Consequently we need to consider this case confirmed."
He urged Germans to avoid contact with birds but insisted the average citizen was in no threat of danger.
The Agriculture Ministry said poultry within nearly 2 miles of where the dead swans were found would be tested.
Agriculture Minister Horst Seehofer urged all farmers to bring their birds inside immediately, if possible, to prevent any contact with migrating fowl. By Friday, all birds will be required by law to be kept indoors.
Germany initially had planned to order all birds indoors for at least two months starting March 1 after authorities discovered H5N1 in dead swans in Italy and Greece — the first time the highly infectious strain had been detected in the 25-nation EU.
Seehofer was meeting with state agriculture ministers and Health Minister Ulla Schmidt later in the day to discuss the situation.
H5N1 also has occurred in birds in Asia, Africa and the Middle East.
Iraq's announcement came a day after neighboring Iran said 135 wild swans died of bird flu in marshlands near the Caspian Sea in the country's first case of the disease. Iran's official Islamic Republic News Agency quoted the country's Veterinary Organization as saying that "international laboratory results" confirmed the swans died from bird flu, though it did not name or give the location of the laboratory.
Minister Abdel Mutalib Mohammed declared the alert after birds suspected of having the disease were discovered in Maysan province, a major southern trade route in Iraq, said Dr. Ibtisam Aziz Ali, spokeswoman for a government committee on bird flu.
Mohammed said the government has to "totally close" Maysan using Iraqi soldiers and police and carry out culling of poultry. He didn't elaborate further on what steps would be taken to close the province.
Maysan includes some of Iraq's famous marshlands, and U.S. and U.N. officials fear the deadly disease could spread rapidly if it reaches the area rich in bird life.
Tests are being carried out at a WHO-approved lab in Egypt on samples taken from about 10 suspected human cases in Iraq, including the deceased uncle of a girl who died Jan. 17 of the disease in Iraq's northern Kurdistan region.
A WHO team arrived in Iraq on Feb. 4 and traveled extensively throughout Kurdistan to learn how the disease was introduced to the country, promote ways to treat it and prevent its spread. It is expected to visit Maysan province.
Experts believe the disease was introduced to Iraq by migratory birds, which follow a southward path through Kurdistan along the Euphrates and Tigris rivers to the southern marshlands, before continuing into Kuwait and Africa.