Since its release, fans have campaigned to have the game's ending changed with a patch or through future DLC.
However, speaking at a Smithsonian panel in Washington DC last week, Levine said that such a move would lead to further disappointment, reports Eurogamer.
Calling it an important moment, Levine said: "I think if those people got what they wanted and [BioWare] wrote their ending they would be very disappointed in the emotional feeling they got because... they didn't really create it.
"This whole thing is making me a little bit sad because I don't think anyone would get what they wanted if that happened."
BioWare Mythic's Paul Barnett also spoke at the event, saying: "If computer games are art than I fully endorse the author of the artwork to have a statement about what they believe should happen.
"Just as JK Rowling can end her books and say that is the end of Harry Potter. I don't think she should be forced to make another one."
> Read our BioShock Infinite interview with Ken Levine
In addition to the online campaign, some fans have filed complaints with the US Federal Trade Commission, citing false advertising from BioWare and Electronic Arts.
The game's director Casey Hudson previously defended its ending, claiming that the polarising conclusion makes it more memorable.
Mass Effect 3 shipped 3.5 million copies worldwide during its first week on sale, making it the biggest entertainment launch of the year, according to publisher Electronic Arts.
Mass Effect 3 is available on Xbox 360, PS3 and PC.
> Read our review of Mass Effect 3
Watch the launch trailer for Mass Effect 3 below: