On Twitter, a fan had asked if he was going to put the game back in the app store.
"Yes. But not soon," Mr Nguyen replied, later adding: "I don't work by plan. I will release it when it is done."
Mr Nguyen removed the popular game in February, saying its popularity had ruined his "simple life".Ruined lives
Launched in May 2013, Flappy Bird was free to download and required players to tap the screen to keep the bird in flight.
Despite its simple graphics, Flappy Bird was a notoriously difficult game since many users could only keep the bird in the air for a few seconds before it hit an obstacle and fell.
The game went viral after being promoted almost entirely by social media users and was reviewed on a YouTube channel by more than 22 million subscribers.
It was downloaded 50 million times, and at the height of its popularity, Mr Nguyen was reportedly earning $50,000 (£30,450) a day from advertising
In an interview earlier this month with Rolling Stone, Mr Nguyen said he was moved to remove the popular mobile game from the App store after users wrote to him detailing how the game had destroyed their lives.
After the game was taken down, users started several passionate petitions to get the game reinstated.