Tokyo Women's Medical University Hospital gave 63 children a powerful anesthetic over a five-year period through 2013 that was banned for use with children, the university said.
The anesthetic is the same one that killed pop star Michael Jackson in an overdose case in 2009.
The university said Thursday it found out that propofol was being used on children hooked up to an artificial ventilator at its hospital in Tokyo's Shinjuku Ward after a 2-year-old boy died in February after being given the drug.
Earlier in the day, Yuichi Takakuwa, head of the university's school of medicine, told a separate press conference that 55 of the 63 children were improperly given the agent intravenously for two days or more, and criticized the hospital's practice as "making light of lives."
Takakuwa said hospital staff did not question the use of the banned agent. Drug makers have urged doctors not to use propofol on children in light of related deaths abroad.
Takakuwa and his staff said the 63 children were 14 or younger and put on ventilators in the hospital's intensive care units between 2009 and 2013.
The university has disclosed only the number of children who were administered propofol, saying it would release other details later.
University professor Toshio Yoshihara, a nose and throat specialist who operated on the 2-year-old boy, said he left the decision on whether to use propofol to an anesthesiologist.
The anesthesiologist was quoted as saying that propofol took effect instantly.
Meanwhile, university chancellor Toshimasa Yoshioka issued a statement saying he did not allow Takakuwa and his staff to hold their press conference, indicating disarray in the hospital's response to the case.
The 2-year-old boy died on Feb. 21 at the hospital, three days after an operation to remove lymphangioma. The hospital reported his death Feb. 25.