Viktor Yushchenko, the president, and key ministers, addressing a meeting after a variant of the virus was detected in domestic fowl in six villages, said on Saturday that Interior Ministry troops would be sent to the zones.
Oleksander Baranivsky, the agriculture minister, described the virus, identified as H5, as lethal and said samples were being sent to laboratories in Britain and Italy for final analysis.
"This is a highly pathogenic virus. Birds are dying from it in no more than two to eight hours," he told a news conference.
"Quarantine restrictions are being introduced in all villages - a 3km zone where entry and exit are banned altogether."
Movements would be restricted in a further 10km monitoring zone in the peninsula jutting into the Black Sea - a key stopping point for migratory birds heading south for the winter.
Residents of affected villages would be checked and their birds destroyed in a four-day operation beginning on Sunday.
"We must ensure that residents are kept informed to avoid all panic," Baranivsky said. "The situation is under control."
Other measures set down in a presidential decree included a ban on sales of privately raised poultry in Crimea, tougher checks of farms and restrictions on transporting livestock.
Ukraine will introduce restrictions
on transporting livestock
President Yushchenko, expected to visit the region on Sunday, sought to reassure Ukrainians.
"Today we must show solidarity and mutual understanding throughout the country and carry out effective measures to combat this illness in the affected region," he told ministers.
The country's top veterinary surgeon, already in the region, said the quarantine would remain in force for 21 days.
"At the moment, there are millions of migratory birds in (Crimea's) Lake Sivash region. They will be flying on to Italy," Petro Verbytsky said. "No cases of human illness have yet been recorded."
Ukraine had previously been declared free of bird flu, though the deadly H5N1 virus had been discovered not far from its borders in Romania and Russia.
The H5N1 bird flu virus is endemic in poultry in parts of Asia where it has killed almost 70 people since 2003 and led to the slaughter of millions of domestic birds.
Many scientists fear that H5N1 could kill millions of people if it mutates into a form that passes easily among humans. But so far, there is no sign the virus has changed in this way and no human cases have been found outside Asia.