According to SNA Japan the tremor was a 4.6 magnitude earthquake off the coast of the Chiba Prefecture, but it was barely felt in Tokyo.
It is unclear why the emergency system was tripped, and the alert left millions of people started in Japan’s capital.
One person tweeted: “JESUS! My iPhone earthquake alert just boomed so loud I thought it was the third impact!!
“Fortunately earthquake didn’t seem to shake my area of Japan too much. But still, phone alert volume was definitely louder than usual.”
Another wrote: “Woken by a massive earthquake alarm on the phone.
“But seems we got no actual shaking in Tokyo.
“Unless we count the people nervously waiting for something to happen – then there’s probably a lot of shaking.”
Another said: “Earthquake warning alarm went off, coupled with creepy warning music from outdoors.
“Didn’t feel a thing in central Tokyo but hope everyone is okay!”
An “extremely loud” earthquake alarm also went off, warning the capital of the risk of a big earthquake.
At 12.15am local time the Japanese Meteorological Agency said it was a 4.6 magnitude earthquake with the epicentre off the coast of the Chiba Prefecture.
James Reynolds, reporter for CNN was in Tokyo when the earthquake alert went off.
He wrote: “For some reason it appears the advance warning system for a major #earthquake was tricked into thinking a big one had happened, thankfully it appears to only be a M4.6 Shindo 4.
“The alert itself is absolutely terrifying, esp at 1220am… #Japan.”