It comes after the operator launched "price trials" in October which led to some huge differences in prices available to agents and online.
Agents received a commercial email detailing the change on Thursday, December 20.
Phil Gardner, Thomas Cook sales and e-commerce director, confirmed: "With more and more customers looking for deals and buying online, we need to compete on a level playing field with other operators and online travel agents.
"As a result, we will be strengthening our web pricing to make sure we offer our online customers the best price possible.”
A spokesperson confirmed to TTG that the prices available to Thomas Cook retail agents would be the same as for independents.
Agents will need to decide whether to price match from their own commission.
TTG will bring you more on this story in due course.
