He told BBC News that attempts to dissuade companies from writing Twitter client applications were about improving the user experience.
Twitter has come under fire for suggesting that it did not want developers creating software which replicated its own interface.
Critics claim it is about ensuring users view adverts on its site.
Since Twitter's creation, scores of third-party applications have appeared that allow users to write, read and respond to tweets.However, in a recent blog posting, Twitter's coding chief Ryan Sarver suggested that companies should consider stopping making such software.
The move was condemned by developers who feel they are partly responsible for Twitter's success and are concerned about how they will make money in the future.
But Mr Stone insisted that the company's focus is about providing a consistent experience for the user, no matter how they access the service.
"Historically the best way to do that is not necessarily to create or recreate apps that could be confusing or do the things we are already doing," he said.
"Developers extend our ability to help users, and our end goal is to serve users. Part of that goal can by helped by giving developers opportunities to create new, interesting and innovative ways to help them get more value out of Twitter." End Quote Biz Stone Twitter co-founder
Too many apps
As an example of the confusion that he believes exists, Mr Stone pointed to the number of Twitter apps available for the iPhone.They include Twittelator, Twitterific, TweetDeck, Echofon, Tweetcaster, La Twit, Tweetaholic, TweetList, TweetBird and TweetBoard.
Mr Stone explained that since Twitter had brought out its own official clients the number of users had skyrocketed.
However, research carried-out by media analytics firm Sysomos suggests that third-party applications are still widely used.
The company looked at 25 million tweets, sent on the day that Twitter unveiled its new policy. It found that 42% were sent from unofficial apps.
"The question for developers is to ask themselves is how they can best serve the users," said Mr Stone.
"By another app that pretty much does the same thing as Twitter? Or by creating new and innovative ways to get value out of Twitter that we are not necessarily doing ourselves," he said.
In the blog posting that sparked the controversy, Ryan Sarver wrote: "Developers ask us if they should build client apps that mimic or reproduce the mainstream Twitter consumer client experience. The answer is no."
He suggested that they should look to build other services that complement the Twitter experience such as mining data to help with brand management, customer relations and enterprise solutions.
While existing applications are fine for the moment, Mr Sarver said they would be closely policed.
Learning curve Developers vented their fury on Twitter's discussion board and various blogs calling the decision everything from appalling to chilling.
RSS pioneer Dave Winer told technology blog GigaOm.com that the new roadmap for developers underscored the need for them to look at building new businesses directly on the internet instead of on other services where the owner is too active.
"The Internet remains the best place to develop because it is the Platform With No Platform Vendor. Every generation of developers learns this for themselves," he said.
Mr Stone said while he understood the frustration and concern emanating from the developer community, Twitter had to do what is best for its users.
"There are going to be some growing pains but I think the most important thing we can do is communicate as best we can, even if it is bad news people don't want to hear or we are not comfortable saying.
"It is important because people can get the clarity they need," he said.