He died on Sunday at home surrounded by his family, his daughter said.
Internationally acclaimed as an outspoken champion of democracy, he "dedicated his whole life to this country through his work", daughter Tatiana Ananta told The Associated Press.
"We all have lost a great father, a great author," she said. "I am very proud of him."
Pramoedya - jailed under successive regimes, including 14 years under ex-president Suharto - was nominated several times for a Nobel Prize in literature and his 34 books and essays have been translated into 37 languages.
His best-known works - the Buru Quartet novels about Indonesia's independence struggle against the Dutch - were written on scraps of paper and surreptitiously smuggled out while he was imprisoned on the remote island of Buru.
Age and deteriorating health - combined with a sense of closure in his work - kept Pramoedya from writing since 2000, though he collaborated with one of his daughters on an encyclopedia of Indonesia.
Grandson Kiki Sepitan said Pramoedya asked to leave Jakarta's Catholic St Carolus Hospital, where he spent two days in intensive care with heart trouble and complications from diabetes, late on Saturday.
Pramoedya died at home
surrounded by friends and family
The author immediately lit up a clove cigarette - he was rarely seen without one - and his condition deteriorated overnight, he said.
Born in 1925 to a rice farmer during Dutch colonial rule, Pramoedya criticised successive governments over more than a half century, even in his last frail years. He reserved his harshest judgment for Suharto, blamed for the death and imprisonment of more than a million Indonesians.
But his ideas - once a major influence fuelling the pro-democracy groundswell that toppled the former dictator - have been largely cast aside as Indonesia struggles to revive its economy, defeat Muslim fighters responsible for a string of deadly bombings, and put down separatist rebellions.
Pramoedya advocated the removal of bureaucrats and politicians "tainted" by Suharto-era abuses, but corruption remains rampant and some of the former president's cronies remain in office even today.
He also wanted an inclusive government that welcomed people from parts of the sprawling Indonesian archipelago outside the main island of Java, but the Javanese still hold the reins of power.
"I am half blind and almost totally deaf, but I won't stop being angry because not many people are outraged enough at the state of Indonesia," he told The AP in 2004.
Pramoedya's harshest judgment
was reserved for Suharto
Pramoedya was first jailed in 1947 by Dutch troops for being "anti-colonialist".
He was later accused of sympathising with Chinese communists and imprisoned again shortly after Suharto came to power in the aftermath of the assassination of right-wing Indonesian generals in 1965.
Pramoedya's left-leaning, outspoken style earned him enemies within Suharto's government and his works were banned from circulation.
He was thrown in a cell without trial, first off the coast of mainland Java, and then in the penal colony of Buru in the eastern islands of the Indonesian archipelago, along with thousands of other opponents of the pro-Western Suharto government.