State television said the Limassol-registered Nordsuk had begun its voyage to Malta in Taiwan. It was not known what cargo it carried. Taiwan found the deadly H5N1 bird flu virus last week in a container of birds smuggled from China, its first case for two years.
Maltese chief vet Merielle Vella told the press late on Sunday that officials were searching the ship and dockers who had been on board would be "decontaminated".
Two dead birds had been found so far and the search was continuing, she said, adding that the birds would be tested for bird flu in Malta and abroad.
No bird flu has been detected in Malta so far. Civil protection, police and health department officials held an exercise on Friday to test their response should a bird flu outbreak be reported.