Waters wrote in a Facebook post Saturday: "Neil? I shall ponder all of this long and hard. We don't really know each other, but, you were always one of my heroes, I am confused.
Last week, Johansson ended her relationship with Oxfam International after being criticized over her support for SodaStream, the Israeli company with a factory in the West Bank.
A statement released by Johansson's spokesman Wednesday said the 29-year-old actress has "a fundamental difference of opinion" with Oxfam because the humanitarian group opposes all trade from Israeli settlements, saying they are illegal and deny Palestinian rights.
Scarlett Johansson in SodaStream commercial
Earlier this month, "The Avengers" and "Her" actress signed on as the first global brand ambassador of SodaStream International Ltd., and she's set to appear in an ad for the at-home soda maker during the Super Bowl on Sunday.
SodaStream has come under fire from pro-Palestinian activists for maintaining a large factory in the city of Ma'ale Adumim, located beyond the Green Line, some 10 minutes from Jerusalem. The factory employs more than 500 Palestinians.
In response to the criticism, Johansson said last week she was a "supporter of economic cooperation and social interaction between a democratic Israel and Palestine."
'What are the equal rights of which you speak?'
Slamming Johansson in his Facebook post, Waters wrote: "Scarlett's choice of Soda Stream over Oxfam is such an act of intellectual, political, and civil about face, that we, all those of us who care about the downtrodden, the oppressed, the occupied, the second class, will find it hard to rationalize.
"Scarlett, I have read your reposts and excuses, in them you claim that the Palestinian workers in the factory have equal pay, benefits and 'Equal rights.' Really? Equal Rights? Do they?
"Do they have the right to vote? Do they have access to the roads? Can they travel to their work place without waiting for hours to pass through the occupying forces control barriers? Do they have clean drinking water? Do they have sanitation? Do they have citizenship? Do they have the right not to have the standard issue kicking in their door in the middle of the night and taking their children away? Do they have the right to appeal against arbitrary and indefinite imprisonment? Do they have the right to re-occupy the property and homes they owned before 1948? Do they have the right to an ordinary, decent human family life? Do they have the right to self determination? Do they have the right to continue to develop a cultural life that is ancient and profound?
"If these questions put you in a quandary I can answer them for you. The answer is, NO, they do not. The workers in The Soda Stream Factory do not have any of these rights. So, what are the 'equal rights' of which you speak?"
In recent years, Waters has been encouraging different artists and musicians not to visit Israel. He has written a letter calling on musicians to avoid performing in Israel, presented an inflatable pig with a Star of David on it in his concert, and voiced radical statements against Israel's policy in the territories. Last December, he even compared Israel to Nazi Germany in an interview.
Before joining the anti-Israel boycott movement, the English musician himself performed in Israel in 2006.
Waters concluded his Facebook post by saying, "Scarlett, you are undeniably cute, but if you think Soda Stream is building bridges towards peace you are also undeniably not paying attention."
The Associated Press contributed to this report