MVRDV said in a statement on its website Monday that it wasn't its intention to create an image evoking the 2001 attacks.
It says it "sincerely" apologizes to anyone whose feelings it has hurt.
The design unveiled in Seoul last week is supposed to show a cloud covering the center of the buildings.
The statement didn't say whether MVRDV will retain the design.
A South Korean business partner says construction is to start in 2013.