Stallman originally planned to visit the region and give some talks in the Palestinian territories, with the costs of his visit being paid for by the Palestinians.
He also scheduled some talks in Israel, at Haifa University and the Shenkar College of Engineering and Design, according to a report in the Israeli newspaper, Haaretz.
In correspondence with the organiser of the Israel part of the trip, Stallman makes it clear that the Palestinians had issued the invitation.
"The funds for my travel to Israel are coming from Palestinians who invited me to give talks for them," Stallman wrote to Edward Aronovich of the Israeli Society for Free and Open Source Software.
"They are unhappy that I offered to give talks at Israeli universities, and say they won't buy the tickets if I'm going to do that. So I can go, and cancel these speeches, or not go, and cancel these speeches."
He added: "I think it is best if I go, and give the speeches they originally invited me to give. I am sorry for the disappointment this will cause."
Aronovich responded: "I am not disappointed that you will not give the talks - That is your legitimate right. When we had the same goals we set it and now we do not. That might happen and even though it is not pleasant it is not totally unacceptable.
"However, personally I start to doubt your truthfulness about freedom. Boycotting the Israeli Universities since you get funds from Palestinians means that you accepted the Palestinians proprietary license. Neither you nor them want to help their neighbor (sic). That is the meaning of what you are doing. Oh boy, you should really re-consider the meaning of freedom given the agreements you make.
"You chose the "Free beer" giving up the "Free of speech" and that disappoints me very much since it has to do with the genuinity (sic) implementation of your own presented ideas."