Scott stated that his 1979 sci-fi classic is very different to the upcoming Prometheus, although he has previously stated that the two films do occupy the same general universe.
Speaking to Total Film, Scott said: "Are there parallels to be drawn? No. The dynamics are entirely different."
Meanwhile, the film's star Noomi Rapace suggested that there are similarities between her character and Alien's heroine Ripley (Sigourney Weaver).
Rapace commented: "I'd say, yes, there are similarities, though I think my character is a bit more feminine, maybe.
"My character and Dr Holloway (Logan Marshall-Green) are the ones who discover something on Earth that gives us the last possible piece to go out on this journey.
"So, I'm carrying more on a personal level than [Ripley] did."
Scott said yesterday that he is determined for the film to be a box office success, and may pursue a PG-13 rating in the US in order to achieve this, in contrast to Alien's R rating.
Prometheus will open in the UK on June 1, and the US on June 8.
Watch a trailer for Prometheus below: