Lived there:
Depends on the company, some places are very western but generally: They bow low and quickly get to work. If your boss comes up, one would say GOMENASAI (sorry), MOUSHIWAKEGOZAIMASEN (so terrible, I have no excuse-words that could be used) but saying something like ‘it’s not my fault…’ is to avoid (should have left earlier – that’s all).
In old fashion companies, one could try catching up by staying late (eg. those using time cards), some will take away 1 hour pay off even if it’s 3 min…
If the subway is late, they give out excuse papers (1min is worth millions, if you kill yourself by jumping in the railway, your family has to pay. – it was fashion at one time, that’s why they put those glass security walls)
Some southern islands are… like every southern island: slow and being late ~30min is custom.