Founded in 1987, the firm popularized the concept of shareware gaming and published the seminal Duke Nukem and Wolfenstein 3D first-person shooters.
The company was working on a follow-up title, Duke Nukem Forever, which after being in development for 12 years has become the object of industry derision.
Publisher, Take-Two says it will no longer fund development of the game but retains rights to the title.
"We can confirm that our relationship with 3D Realms for Duke Nukem Forever was a publishing arrangement, which did not include ongoing funds for development of the title," said Take-Two's Alan Lewis in a statement.
There has been no official comment from 3D Realms, other than a forum posting from the company's webmaster, Joe Siegler, who said: "It's not a marketing thing. It's true. I have nothing further to say at this time."
Other companies with links to 3D Realms or the Duke Nukem series were quick to distance themselves.
In a posting on Twitter, Apogee Software said it was "officially not affected by the situation at 3DRealms".
"Development of the Duke Nukem Trilogy is continuing as planned and further announcements about upcoming games will be made in the near future," the statement added.
Guardian newspaper games writer Steve Boxer said it was astonishing 3D Realms had not finished the game after more than a decade of development.
"It would have been nice to see another Duke Nukem game, but given they had more than 12 years it's just incompetence of the highest order.
"3D Realms made some great games in the past, but they got overtaken by the 21st Century.
"Sadly, Duke Nukem Forever was the most aptly named title in the history of games. Now, it's just Duke Nukem Never."