The science fiction superhero film features music from Grammy nominee Akon, as well as cameos from Amitabh Bachchan and Rajinkanth.
A source told The Times of India: "Either Shah Rukh was busy with the post-production of RA.One or Lady GaGa's dates couldn't be worked out.
"The song couldn't be shot for the film, although composers Vishal-Shekhar had already composed a tune for Lady GaGa to record."
Director Abuhav Sinha confirmed that the Bollywood veteran had been in touch with the international pop icon.
"Shah Rukh was very keen on working with Lady GaGa," Sinha said. "In fact, we were supposed to shoot them together for a song that would have been used with the end titles of Ra.One.
"However, we couldn't co-ordinate Shah Rukh and Lady GaGa's dates. The idea of bringing them together is still very much alive. We're working on something."
In September, Khan said that he started listening to Lady GaGa in order to reinvent himself.
The actor also reportedly planned an international tour with Akon, who sings title track 'Chammak Challo'.
