The rumours were sparked by Dutt's special visit to the set of the film that marks the comeback of actress Aishwarya Rai Bachchan.
Calling the speculation "bizarre," Gupta tweeted, "BAAVLE ho gaye hain kya sab? (Has everyone gone mad?) Where do these bizarre rumours even stem from?" He also retweeted an apparent clarification by Dutt's spokesperson.
Dutt, 56, who is out on a 30-day parole, has previously collaborated with Gupta for movies like "Kaante", "Zinda" and "Jung".
The duo last worked together in the 2007 movie "Dus Kahaniyaan", an anthology of ten short films, where Gupta directed the "Vaastav" actor in a segment called "Rise & Fall".
"Jazbaa", also starring Irrfan Khan and Shabana Azmi, is slated to hit theatres on October 9.