The unnamed 64-year-old, who works at the public waterworks bureau in the southwestern city of Kobe, had consistently left his desk early to buy his lunch, Japan's Asahi Broadcasting Corporation reported last week.
A spokesperson for the waterworks bureau told Agence France-Presse on Thursday: "The lunch break is from noon to 1pm. He left his desk before the break."
This happened 26 times between September 2017 and March 2018, meaning a total of 78 minutes was lost to early breaks.
The man was discovered after a colleague looked out the window one day and spotted him leaving the building early, Asahi said.
The 64-year-old reportedly wanted a "change of pace" from the Japan's workplace norms.
Workers are typically expected to eat lunch at their desks, stay in the office until after the boss leaves, and go to work even if they don't feel well, according to Sora News 24, a news site focused on Japan. It is not clear what time the man returned from those lunch breaks.
Regardless, the waterworks bureau has refused to let the lost 78 minutes slide. They docked him half a day's pay, and held a televised press conference to apologise for the employee's behaviour.
The press conference included four city officials delivering their apologies and bowing deeply for at least four seconds, a traditional sign of apology in Japanese culture.
Here's a video:
One official at the conference said, according to Sora News 24: "It's immensely regrettable that such a scandal took place, and we wish to express our sincere apologies."
There is no indication that the public in Kobe had demanded the apology.
Many workers in Japan are under extraordinary pressure to work long hours, and hundreds of people have died of organ failures or from taking their own life as a result of overwork.
Karoshi, a Japanese word that literally means "death by overwork," is recognised by the Japanese government as an official cause of death.
Japanese society is also fixated on punctuality. Last month a railway company issued an official apology after leaving the station 25 seconds early, departing at 7:11:35am instead of the scheduled 7:12am.
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