The song appeared online earlier this week, prompting the filmmaker to share the track, even though he had cut it from the movie.
Kunder wrote on Twitter: "We've not been able to stop 'I Want Fakta U' Song from spreading. So may as well enjoy it."
Farah Khan also took to the social networking site to comment that the song had been retitled, explaining: "I Want Fakht U [changed] to I Want Just You sometime ago. This is the old version thats leaked (sic)."
Khan later added: "Trying to do damage control since morning."
Playback singer Sunidhi Chauhan has provided vocals in both versions of the track.
The first official trailer from the Akshay Kumar and Sonakshi Sinha alien-themed movie has amassed over 500,000 YouTube views in its first few days of release.
Kunder had originally planned to release the film after his debut Jaan-e-mann, but instead worked with Khan on the comedy Tees Maar Khan.
Listen to the leaked track from Joker below: