Rowling, one of Britain's most successful female writers said she was opposed to a wider cultural boycott of Israel after a number of her fans used her Harry Potter characters to argue in favour of a total cultural boycott of the nation.
She wrote on Twitter: "The Palestinian community has suffered untold injustice and brutality. I want to see the Israeli government held to account for that injustice and brutality.
Rowling further said that Harry Potter fans had used her characters to make points about the boycott.
She said some readers pointed out that "talking" did not stop the "Wizarding war" in her popular novels and drew parallels between the Harry Potter plot-lines and the conflict in the Middle East.
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The author stressed: "What sits uncomfortably with me is that severing contacts with Israel's cultural and academic community means refusing to engage with some of the Israelis who are most pro-Palestinian, and most critical of Israel's government.
Referring to the character of Snape, who is persuaded to swap evil for good, she said: "The course of my fictional war was forever changed when Snape chose to abandon the course on which he was set."
Fans praised her evaluation of the conflict, and wrote a series of replies in support.