Their employer, general goods store Habita, has apologised for the deaths, describing them as the "loss of two precious lives."
The two employees were among 38 people who died in the magnitude 6.8 earthquake that struck Kumamoto Prefecture on 28 July. Seven of the fatalities were from Aeon Mall.
According to NHK, Habita sales director Goji Yuse admitted the decision was wrong.
"The instructions given at the time were inappropriate, and I truly regret them," Yuse said.
One of the workers has been identified as 22-year-old Kurumi Otake. The identity of the second employee has not been made public.
Otake's family told local media that she met a relative outside Aeon Mall after the earthquake. She reportedly told the relative she had to return to the building because her employer had instructed her to move money from the cash register into a safe.
The account was confirmed by two company representatives who attended Otake's wake on Sunday and apologised to her family.
Yuse said the company was considering how to proceed with the matter.
"Looking back now, it was not worth a life," he told reporters at the wake, according to Kyodo.
Otake's relative described her as someone with a "strong sense of justice". She had supported her mother after her father died three years ago, Asahi Shimbun reported.
"If she hadn't gone back inside the store at that time, Kurumi would still be with her family today," the relative said.
While most people in Aeon mall had evacuated shortly after the earthquake, some employees were still in the building about an hour later, when an explosion ripped through the mall.
"My daughter is not coming back," local media reported her mother as saying.
Habita, founded in 1976 and operates more than ten stores across several prefectures.
