The wheelchair-bound Hawking, who has won international recognition for his work on black holes, had been due to speak at a prestigious conference in June organized by Israeli President Shimon Peres that draws hundreds of leading world figures.
However, his name was quietly dropped from the list of participants earlier this week, giving a major boost to supporters of pro-Palestinian groups that want to isolate Israel on the international stage over the continued occupation.
"This is his independent decision to respect the boycott, based upon his knowledge of Palestine, and on the unanimous advice of his own academic contacts there," the British Committee for the Universities of Palestine said on its website.
Cambridge University, where Hawking works, confirmed that the statement had been approved by the professor. Hawking did not issue any statement in his own name.
The conference organizers criticized Hawking's decision.
"The academic boycott against Israel is in our view outrageous and improper, certainly for someone for whom the spirit of liberty?? ??lies at the basis of his human and academic mission," conference chairman Israel Maimon said in a statement.
By snubbing the annual president's conference, which is due to be addressed by former U.S. President Bill Clinton and former British Prime Minister Tony Blair, Hawking has become one of the prominent scientists to join the boycott movement.
Numerous figures from the world of art and entertainment have also refused to perform in Israel in recent years as part of an effort to promote the Palestinian cause, including British singer Elvis Costello and U.S. indie rock band the Pixies.
Direct peace talks between Israel and the Palestinians broke down in 2010 over the issue of continued Jewish settlement building on land seized in the 1967 war. Palestinians want to create an independent state on the captured territories.
The United States is seeking to revive the negotiations.
(Additional reporting by Estelle Shirbon in London, Writing by Crispian Balmer, Editing by Jeffrey Heller)
