The South African-born author, who is now an Australian citizen, made the comparison in a speech prepared for delivery at the opening in Sydney Thursday of an art exhibition entitled "Voiceless: I feel therefore I am".
The Holocaust was a "warning on the grandest scale that there is something deeply, cosmically wrong with regarding and treating fellow beings as mere units of any kind," Coetzee said, in an extract published in the Sydney Morning Herald.
Coetzee, a vegetarian, wrote that most people have an equivocal attitude to the industrial use of animals.
"They make use of the products of that industry, but are nevertheless a little sickened, a little queasy, when they think of what happens on factory farms and abattoirs.
"Therefore they arrange their lives in such a way that they need be reminded of farms and abattoirs as little as possible, and they do their best to ensure their children are kept in the dark too, because children have tender hearts and are easily moved."
The Nobel committee, naming Coetzee as the winner of the 2003 prize for literature, described him as "ruthless in his criticism of the cruel rationalism and cosmetic morality of western civilisation."
He was the first author to be awarded the Booker Prize twice: first for "Life and Times of Michael K" in 1983, and again for "Disgrace" in 1999.
Coetzee wrote that "in the 20th Century, a group of powerful and bloody-minded men in Germany hit on the idea of adapting the methods of the industrial stockyard, as pioneered and perfected in Chicago, to the slaughter – or what they preferred to call the processing – of human beings.
"Of course we cried out in horror when we found out what they had been up to. What a terrible crime to treat human beings like cattle – if we had only known beforehand. "But our cry should more accurately have been: what a terrible crime to treat human beings like units in an industrial process.
"And that cry should have had a postscript: what a terrible crime – come to think of it, a crime against nature – to treat any living being like a unit in an industrial process."
Coetzee wrote that the efforts of the animal rights movement "are rightly directed at decent people who both know and don't know that there is something going on that stinks to high heaven." "These are people who will say: 'Yes, it's terrible what lives brood sows live; it's terrible what lives veal calves live,' but who will add, with a helpless shrug of the shoulders – 'what can I do about it?'"
"The task of the movement is to offer such people imaginative but practical options for what to do next after they have been revolted by a glimpse of the lives factory animals live and the deaths they die."
Children offered the brightest hope, he wrote: "It takes but one glance into a slaughterhouse to turn a child into a lifelong vegetarian."