The Yomiuri Shimbun reports that police are looking into whether the action constitutes a crime.
The drop-off, named Konotori-no-Yurikago (Stork's Cradle), was conceived as a way for parents to safely abandon a newborn baby for whom they cannot care.
However, the child dropped off at the hospital on Thursday did not fit the hospital's definition of a baby, and there have been an increasing number of observers that say the drop-off's existence may have encouraged the father to abandon his child.
The baby hatch began operation at noon last Thursday. According to sources, the boy was left at the hospital two or three hours later. The boy told hospital workers his name and age, and said his father had brought him there. Based on the boy's account, it is believed he was brought there from outside the prefecture.
The boy was reportedly in good health, but had nothing with him that indicated where he was from.
The police are currently searching for the boy's home and plan to question his parents when they are found.
"Even if this is true - even if it isn't - as a member of the medical profession, I can't comment on this," the hospital's vice director, Taiji Hasuda, said.
The Kumamoto city government, which approved the drop-off on 5 April, also said it could not comment on the report.
While some people say the drop-off is an attempt to save lives, there are those who feel that it will merely offer a way for parents to shirk their responsibilities. For this reason, the hospital is urging parents considering the drop-off to first seek consultation.
The baby hatch is located along a wall on the first floor of the hospital. It has a 50x60cm door that can be opened from the outside, while on the inside there is an incubator to help a baby survive.
When the door is opened, it triggers a buzzer at the nurses station, while a closed-circuit camera monitors the incubator as a doctor or midwife go to help the infant.
Melbourne baby recovering
The news comes as Melbourne police appeal for the mother of a newborn left outside a Victorian hospital on Mother's Day to come forward.
According to the Sydney Morning Herald, the baby girl, who staff named Catherine, was still suffering from hypothermia but was improving rapidly after she was transferred to an incubator in intensive care at Melbourne's Royal Children's Hospital.
The NSW Department of Community Service is urging any pregnant women or new mothers to seek support before taking the drastic step of abandoning their child.
Boy, 3, dropped off at baby hatch (Daily Yomiuri Online, 16/5/07)
Toddler left at new baby hatch - reports (News.com.au, 16/5/07)
Boy dumped in Japan's unwanted baby box (The Age, 16/507)
Plea to mothers as dumped baby makes strong recovery (Sydney Morning Herald, 15/5/07)
LINKS (not necessarily endorsed by Church Resources)
Baby hatch (Wikipedia)
Japanese hospital tests baby hatch (CathNews, 3/5/07)
Priest spearheads Gold Coast mother- baby reunion effort (CathNews, 12/3/07)
Mothers without a choice (Sydney Morning Herald, 16/5/07)
How could they? (The Age, 16/5/07)
16 May 2007