"Are people not even allowed to go to the toilet now? This is like workplace slavery or something," one Twitter user wrote.
While another said: "The punishment is totally absurd – 26 times over a six-month period means he only left the office once a week."
"Absolutely ridiculous – arranging this formal apology with the press would've wasted more time than the three minutes he spent buying his lunch every now and then."
The case reignited a debate over the nature of Japanese work culture - where employees rarely take sick days and work incredibly long hours.
Nearly a quarter of Japanese companies have employees working more than 80 hours overtime a month, often unpaid, a recent survey found. And 12 per cent have employees breaking the 100 hours a month mark.
Workers are entitled to 20 days leave a year but currently about 35 per cent don't take any of it.