Along with André Brink and Breyten Breytenbach, Coetzee was, according to Fred Pfeil, at "the forefront of the anti-apartheid movement within Afrikaner literature and letters". On accepting the Jerusalem Prize in 1987, Coetzee spoke of the limitations of art in South African society, whose structures had resulted in "deformed and stunted relations between human beings" and "a deformed and stunted inner life". He went on to say that "South African literature is a literature in bondage. It is a less than fully human literature. It is exactly the kind of literature you would expect people to write from prison". He called on the South African government to abandon its apartheid policy. Scholar Isidore Diala states that J. M. Coetzee, Nadine Gordimer and André Brink are "three of South Africa's most distinguished white writers, all with definite anti-apartheid commitment".
It has been argued that Coetzee's 1999 novel Disgrace allegorises South Africa's Truth and Reconciliation Commission. Asked about his views on the TRC, Coetzee has stated: "In a state with no official religion, the TRC was somewhat anomalous: a court of a certain kind based to a large degree on Christian teaching and on a strand of Christian teaching accepted in their hearts by only a tiny proportion of the citizenry. Only the future will tell what the TRC managed to achieve".
Following his Australian citizenship ceremony, Coetzee said that "I did not so much leave South Africa, a country with which I retain strong emotional ties, but come to Australia. I came because from the time of my first visit in 1991, I was attracted by the free and generous spirit of the people, by the beauty of the land itself and – when I first saw Adelaide – by the grace of the city that I now have the honour of calling my home." When he initially moved to Australia, he had cited the South African government's lax attitude to crime in that country as a reason for the move, leading to a spat with Thabo Mbeki, who, speaking of Coetzee's novel Disgrace stated that "South Africa is not only a place of rape". In 1999, the African National Congress submission to an investigation into racism in the media by the South African Human Rights Commission named Disgrace as a novel exploiting racist stereotypes. However, when Coetzee won his Nobel Prize, Mbeki congratulated him "on behalf of the South African nation and indeed the continent of Africa".
Coetzee has never specified any political orientation, though has alluded to politics in his work. Writing about his past in the third person, Coetzee states in Doubling the Point that:
Politically, the raznochinets can go either way. But during his student years he, this person, this subject, my subject, steers clear of the right. As a child in Worcester he has seen enough of the Afrikaner right, enough of its rant, to last him a lifetime. In fact, even before Worcester he has perhaps seen more of cruelty and violence than should have been allowed to a child. So as a student he moves on the fringes of the left without being part of the left. Sympathetic to the human concerns of the left, he is alienated, when the crunch comes, by its language – by all political language, in fact.
Asked about the latter part of this quote in an interview, Coetzee said:
There is no longer a left worth speaking of, and a language of the left. The language of politics, with its new economistic bent, is even more repellent than it was fifteen years ago.
In 2005, Coetzee criticised contemporary anti-terrorism laws as resembling those employed by the apartheid regime in South Africa: "I used to think that the people who created [South Africa's] laws that effectively suspended the rule of law were moral barbarians. Now I know they were just pioneers ahead of their time". The main character in Coetzee's 2007 Diary of a Bad Year, which has been described as blending "memoir with fiction, academic criticism with novelistic narration" and refusing "to recognize the border that has traditionally separated political theory from fictional narrative", shares similar concerns about the policies of John Howard and George W. Bush.
In recent years, Coetzee has become a vocal critic of animal cruelty and advocate for the animal rights movement. In a speech given on his behalf by Hugo Weaving in Sydney on 22 February 2007, Coetzee railed against the modern animal husbandry industry. The speech was for Voiceless, the animal protection institute, an Australian non-profit animal protection organization, of which he became a patron in 2004. Coetzee's fiction has similarly engaged with the problems of animal cruelty and animal welfare, in particular his books Disgrace, The Lives of Animals, Elizabeth Costello and in the short story The Old Woman and the Cats which has as its protagonist Elizabeth Costello. He is vegetarian.
Coetzee wanted to be a candidate in the 2014 European Parliament election for the Dutch Party for the Animals. His candidature was however rejected by the Dutch election board, which argued that candidates had to prove legal residence in the European Union to be allowed.