Mehmet Ozkan, the head of the local health directorate, said a medical investigation was under way to determine the cause of the deaths.
Professor Gazi Yigitbasi, the hospital's chief physician, said: "Under normal conditions, we lose five or six babies in three days and less than 20 in a month."
The NTV news channel said a team of doctors from universities in Izmir would inspect the hospital while tests were being done on samples taken from the unit where the babies died.
The incident is the latest in a number of deaths in recent years that have raised questions over standards in newborn units.
In August, a state hospital in Ankara, the capital, reported that 27 newborns had died over a 15-day period.
The hospital said at the time that a variety of reasons were to blame, including hypertension, heart failure and complications at birth. Trade union officials however blamed the deaths on an infection triggered by poor hygiene.
In 2005, eight premature babies died of a bacterial infection in a hospital in the northwestern city of Edirne, and an infection claimed the lives of seven babies at a newborn unit in the central city of Kayseri.