Goalkeeper Courtois joined Chelsea for £7 million from Genk in 2011 and has spent three successive seasons on loan at Atléti, where his arrival has coincided with the Spanish club's resurgence under coach Diego Simeone.
Atlético defeated Barcelona in their Champions League quarter-final to reach their first European semi-final in 40 years on Wednesday night, but a clause in the Belgian's contract means Atlético may have to pay up to €3m if they want to field him against José Mourinho's side.
Courtois is regarded as one of the best goalkeepers in the world already
"It is a figure that we cannot pay," Atlético Madrid president Enrique Cerezo told Spanish radio station Onda Cero.
Courtois was allowed to play against Chelsea in Atlético's 4-1 2012 Super Cup win because no clause was stipulated preventing him from featuring in the European football curtain-raiser.
Should Atlético draw Chelsea in the last four, the likelihood is 34-year-old Daniel Aranzubia will deputise for Courtois, who has two years remaining on his Stamford Bridge contract.
Only 22, Courtois is already regarded as one of the best goalkeepers in the world and has been linked with a permanent move to Atlético, as well as a transfer to Barcelona.
He has won the Europa League and Copa del Rey at the Vicente Calderón, and Atlético are currently first in the Primera Liga with six games remaining.