The two companies had previously revealed plans to collaborate on an attraction, and Angela Jobson from Merlin told BBC Newsbeat conversations on the project date back about eight years.
Merlin has faced complaints from customers about issues such as queues and ride closures at its recent Alton Towers opening weekend.
Jobson said it was still planning investment in its other parks and the company “wasn’t pulling money just to put it into Minecraft”.
But she insisted the new attraction would be “game changing” and elevate the park at Chessington.
“It just allows us to create something different for our guests, and a brand like Minecraft, which has sort of transcended being a game,” she said.
Jobson said the goal was to create something that would appeal to all park visitors, but acknowledged “it’s got to be really credible for people that know and love this game already”.
Merlin will soon face competition from Universal Studios UK, which is expected to open near Bedford in 2031.
Jobson said the company “welcome the competition”.
“We see that as being a really positive thing for the visitor economy in the UK,” she said.