The band recently posted a letter on their Web site claiming that Wilson's Dupree character was based on their Grammy-winning song, "Cousin Dupree," about a couch-hopping houseguest.
In a statement released by his spokeswoman, Ina Treciokas, Wilson said: "I have never heard the song `Cousin Dupree' and I don't even know who this gentleman, Mr. Steely Dan, is. I hope this helps to clear things up and I can get back to concentrating on my new movie, `HEY 19.'"
Larry Solters, a spokesman for the band's management company, did not immediately return a call for comment.
Steely Dan released a string of hits in the '70s, including "Hey Nineteen," "Reeling in the Years" and "Rikki Don't Lose That Number."
"There are some pretty heavy people who are upset about this whole thing and we can't guarantee what kind of heat little Owen may be bringing down on himself," band leaders Walter Becker and Donald Fagen wrote in the letter.
The band asked Wilson, 37, to appear at a concert to apologize to their fans.
"You, Me and Dupree" co-stars Kate Hudson and Matt Dillon as a newlywed couple annoyed by Dupree, a friend who crashes on their couch.
In 2001, "Cousin Dupree" won a Grammy for best pop performance by a duo or group from Steely Dan's album "Two Against Nature," which snagged album of the year.