Mr Chauhan completed his tenure in March. His appointment had triggered student protests at the Pune-based institute. Mr Kher had then said that the FTII needed a person with much more qualifications than Mr Chauhan had as a producer, director or actor.
On Wednesday, Mr Chauhan, however, extended his good wishes to Mr Kher.
"I convey my good wishes to him and I want to move on in life. What happens is that when somebody is given a post, then there are a lot of options behind it. I was also appointed from different options. A lot of people didn't get to see my work. In FTII, it's more important to be a good administrator than a good actor," Mr Chauhan told IANS.
"He is quite experienced and runs his own (acting) institute (Actor Prepares) in Mumbai. So, I think he will be able to handle it quite nicely. I wish all the best to Anupamji and wishes he will complete all the work, which I left due to the end of my chairmanship," he added.
His appointment was followed by massive protests by FTII students and ex-students and a 139-day strike demanding his removal from the post.
Mr Chauhan, who said he himself had a "lot of administrative qualifications", insisted that he had not been axed as claimed by a section of the media.
"I have run the administration of the Cinema and Television Artists Association for 22 years. That's why I was able to do a lot of work during my tenure. The CAG report, which was submitted in Parliament has a line, 'The best work at FTII was done under the chairmanship of Gajendra Chauhan.' That's like a certification of my work. What else do I need?" he said.