Sources within the BBC recently tipped Stephenson to take over digital channel BBC Three from Danny Cohen, who has moved to head up BBC One.
However, Stephenson said in an email sent to independent production companies last week that he wanted to "set the record straight", reports The Guardian.
Stephenson told the producers that he has "ambitious plans for the next few years", and is happy to remain at BBC drama. He acknowledged that it was an unusual approach to send the message, but he wanted to assure the sector that he had not applied to lead BBC Three.
A source at an independent production firm said: "There have been rumours about Ben and the BBC Three job but drama seems a bigger role to me. It seems to be a bit soon for him to move on with so much going on in BBC drama."
The second round of interviews for the BBC Three job is going ahead this week, managed by the outgoing director of BBC Vision Jana Bennett.
Last week, it was reported that BBC entertainment commissioning editor Karl Warner was the frontrunner for the £225,000-a-year post.
However, several external candidates are also thought to be in the running, including ITV director of digital channels and acquisitions Zai Bennett, UKTV controller Matthew Littleford and E4 controller Angela Jain.