The London-based rights group's report, titled "Destination: Occupation," said rental sites Airbnb, Booking.com, Expedia and TripAdvisor are driving tourism to settlements that most of the world considers illegal.
Airbnb announced last November that it would remove West Bank settlement listings but has yet to implement its decision. The company says it is working to identify the "precise boundaries" of areas subject to the policy.
Amnesty called on Airbnb to immediately implement its ban and to extend it to East Jerusalem.
On Twitter, Minister Gilad Erdan called the Amnesty statement "an outrageous attempt to distort facts, deny Jewish heritage & delegitimize Israel."
The World Jewish Congress said it was disheartened by Amnesty's report and called on it to shift its focus back to human rights.
"Amnesty International is a serious and respected human rights organization, whose work to stop abuses around the world should never be underrated, but its singular focus on corporate entities doing business in Israeli settlements is gravely misguided," said WJC CEO and Executive Vice President Robert Singer.
"If Amnesty wishes to involve itself in the Israeli-Palestinian conflict, it should center its attention on the real human rights abuses ongoing in Palestinian territories, and not attack corporate businesses who strive to bridge divides and build peace through global tourism and interaction."