It refers to failing organizations and how the blame of it should be on its ‘head’ that is its leadership.
It does not talk about the biology of the fishes and should not be used as a literal meaning. This is because an actual fish starts to rot from its guts and not head according to piscine biology.
The company was bound to be closed sooner or later considering the kind of mangers that they had hired. A fish rots from the head down after all.
A leader has to be of a strong will and good character otherwise as it is said, the fish rots from the head down. The whole organization would then have to suffer because of it.
His maid servant doesn’t do anything as asked for. But the fish rots from the head down, look at how unorganized his own life is.
There is no origin for this idiom
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definition
Common phrase that has a specific meaning.