The Roman Catholic hospital set up the hatch in May in a bid to prevent abortions and unwanted children. It looks like a mailbox with pictures of storks and is modelled on a similar idea in Germany.
Conservative Prime Minister Shinzo Abe has expressed outrage at the baby drop-off, saying it encourages irresponsibility, but he could find no legal grounds on which stop it being installed.
The hospital has declined to say how many children it has received, but reports said seven have been deposited.
The latest was a week-old boy dropped off last month, Jiji Press and the Yomiuri Shimbun reported.
The southern city of Kumamoto, where the hatch is located, said a help hotline it set up on May 7 amid the controversy had received 357 consultations, with 64 people coming in person.
Most callers talked about unexpected pregnancies or difficulties raising children and many of the people seeking advice were from out of town, said municipal official Shinichiro Yamada.
"It seems that there are women all over the country who are troubled with pregnancy. I hope similar hotlines will be set up in other cities very soon," Yamada said.
Abortion is widely accepted in Japan, where adoption outside the extended family is rare. The country is struggling to reverse a decline in population as more young people decide to delay starting families.