The official version, created by Vietnam-based creator Dong Nguyen, is currently only available for Apple and Android devices.
But the publisher of the Windows Phone version is given as IG Mobile.
Flappy Bird has been downloaded more than 50 million times.
Launched in May 2013, the game has surged in popularity, promoted almost entirely by social media users, and is now the number one free game in the Apple App Store and Google Play Store charts.Windows Phone version of the Flappy Bird game
On Friday, Dong Nguyen Tweeted: "I would like to [say] sorry WP [Windows Phone] users for the late of WP build. I am trying hard to make it happen."
When the BBC alerted Microsoft to the issue, a spokesman said the company was investigating.Exasperating
The game, which took just two to three days to create, is now raking in nearly $50,000 a day in advertising revenue, Mr Nguyen said in an interview.
Players have been sharing pithy and humorous reviews of the game via Twitter and other social media platforms, recounting their exasperation at its apparently addictive qualities.
Its popularity grew even further when one YouTube channel with more than 22 million subscribers reviewed the game.Vietnam-based Dong Nguyen says he has been overwhelmed by the media interest in him and his game
It is the kind of viral social media marketing campaign big games makers can only dream of, so much so that some have accused Mr Nguyen of manipulating the charts using paid-for promotions or robots.
He has denied using any such techniques in email exchanges with Chocolate Lab Apps, a blog about iPhone app development, putting his success purely down to "luck".