"A member of the crew of the ship MV Ocean Wind, Indian citizen Shaikh Rafikque, died in Klaipeda today. The suspected cause of death is bird flu," a statement from the ministry said.
If the deadly H5N1 strain of bird flu is confirmed as the cause of Mr Rafikque’s death, it would be the first human case of the disease in the European Union.
"Rafikque, who was the ship's cook, fell ill on February 4, according to reports from the crew," the ministry said.
"He died in a medical emergency vehicle today," it added in the statement.
The Liberian-flagged Ocean Wing came to Lithuania from Germany on January 17 to undergo repairs.
No autopsy
Although the health ministry had earlier said a preliminary autopsy would be conducted, it later retracted that statement, saying instead that the ship's captain, also Indian, has "not given permission for an autopsy, on religious grounds".
Doctor's at Klaipeda morgue, where the body of the 62-year-old sailor was being held, confirmed that no autopsy has been carried out.
Kazimieras Lukauskas, head of Lithuania's state veterinary and food service, said raw poultry was among food loaded onto the ship in Germany, but played down the possibility that it was the cause of the sailor's death.
"We do not think that poultry used for food on the ship could be the cause of death" Lukauskas said.
A special emergency team has been sent to Klaipeda to disinfect the ship, which had 30 crew members, 29 Indians and one Ukrainian, on board, he said.
Crew members will now undergo examination.