The project will be produced by KriArj Entertainment and Vishal Bhardwaj Pictures.
Bhardwaj said in a statement: "Due to different artistic visions of the film, Honey (Trehan) and I jointly came to the decision that it would be best if I took over as director and saw it through to the end."
Trehan, who has worked closely with Bhardwaj over the years, was to make his directorial debut with the film.
He said: "Owing to our differences in creative understanding, we have mutually and amicably decided that it would be best for our film if Vishal sir took over as director."
Prernaa Arora of KriArj Entertainment said she respects the decision, which is only meant for the "betterment of the film".
Trehan will direct another project in the near future, and it will also be produced by Vishal Bhardwaj Pictures and KriArj Entertainment.
For now, the shoot of the Irrfan and Deepika movie will begin end of February.