Twitter users posted pictures of the mysterious foam, with one calling it "disgusting".
"I saw it just after the earthquake," said Kazuki Nabeta, who lives in the busy central district of Tenjin, where the bubbles were found.
地震で地下から泡は出るわ(福岡天神)ラウンドワン上のピンは落ちてくるわコンビニの中はグッチャグチャになるわ大変やな......地震ってあんまり経験してないから気おつけとこ、皆さんもお気をつけて pic.twitter.com/5lQNuyK0Sd— ロキア (@R0KlA) April 15, 2016
"People were posting pictures on Twitter and it was near my house, so I went out to have a look," said Mr Nabeta.
"There was a fire engine there. There wasn't anything special about it - it was normal foam."
Residents of Fukuoka reported strong shaking but little damage from the two quakes, which took place on Friday and Saturday.
At least 29 people have been killed by the earthquakes, which injured more than 1,500 and left many more homeless.
A spokesperson at the Fukuoka town hall said they did not know anything about the bubbles, which remain a mystery.