About 40 percent of Yamato's 3,924 courier service bases failed to follow the company's procedure for managing the temperature of packages that need to be kept refrigerated or frozen, many of them during the busy summer season.
The company released the outcome of an in-house probe Thursday after it was found last month to have engaged in sloppy temperature management when delivering chilled packages.
Yamato Holding Co.'s "cool" delivery service allows customers to send items such as perishable foods at temperatures of 10 degrees or lower for an extra charge.
To prevent a recurrence, Yamato said it will start limiting the amount of packages that it accepts during busy periods. The company will also send staff responsible for service quality management to service locations nationwide and install monitoring cameras to check whether packages are handled properly.
To clarify management's responsibility, President Masaki Yamauchi will take a 10 percent salary cut for six months. Other board members' salaries will also be reduced, the company said.
"I deeply apologize for causing situations that betray customers' trust," Yamauchi said at a news conference in Tokyo.
According to Yamato, it either compensated for or exchanged items in 7,846 packages during the April-September period.
In a case similar to Yamato's, Japan Post Co. said earlier in November that some of its chilled packages were actually delivered at normal temperature.