Kanai said he was worried that he wouldn't fit in his spacecraft on his return home.
He tweeted: "Good morning, everybody. I have a major announcement today. We had our bodies measured after reaching space, and wow, wow, wow, I had actually grown by as much as 9cm!
"I grew like some plant in just three weeks. Nothing like this since high school. I'm a bit worried whether I'll fit in the Soyuz seat when I go back."
The Russian-built craft Soyuz, which transports astronauts to and from Earth, has a seating height limit.
Although most people who go to space experience the growth phenomenon, they do not stay taller when they go back to Earth, where gravity forces vertebrae to close together.
Kanai, on his first space mission, was previously a diving medical officer with the Japan Maritime Self-Defence Force.