Culture Minister Miri Regev commented: "I was sad to hear that Portman fell like a ripe fruit into the hands of BDS supporters."
But in a clarifying statement, Ms Portman said: “I chose not to attend because I did not want to appear as endorsing Benjamin Netanyahu, who was to be giving a speech at the ceremony.
“Like many Israelis and Jews around the world, I can be critical of the leadership in Israel without wanting to boycott the entire nation. I treasure my Israeli friends and family, Israeli food, books, art, cinema, and dance.”
Ms Portman had notified the foundation that she planned to donate the prize money to international and Israeli organisations dedicated to women’s causes. Israeli philanthropist Morris Kahn - who had promised her an additional $1 million - has criticised her decision not to attend.
Past recipients of the prize include Michael Bloomberg, Michael Douglas and Itzhak Perlman.