The East Asian country has been hit with 11 earthquakes in the last 10 years.
Japan was rocked by the Fukushima earthquake in 2011, which killed more than 20,000 people.
But it came a year after dozens of the fish featured heavily in mythology, known as oarfish, washed up which many treated as omens.
They generally live near the bottom of the oceans and only come to the surface when a disaster nears, according to the myth.
And footage has emerged of one caught by a fisherman this week.
In the clip, the fish has been laid on a table.
It has a long red fin and massive eyes in a bizarre shape.
The cameraman touches the scales of the creature, which let off a residue.
This was one of two of the creatures caught in fishnets, which measured between three and four metres.
Oarfish can grow as long as 11 metres.
The creatures are traditionally known as “Ryugu no tsukai” in Japanese, or the “Messenger from the Sea God’s Palace”.
And the Japanese believe they are indicators of doom when they come to the surface.
The Satomi Higa of the Yomitan’s fisheries cooperative association told CNN: “The two oarfish were swimming vigorously in the nets.
“They looked mysterious and beautiful.”
And the omens point to another potential earthquake.
A number of dead oarfish washed up in Japan and Peru earlier this year, increasing fears of an incoming natural disaster in the country.
It reflects the 2011 Fukushima earthquake and subsequent tsunami, which killed more than 20,000 people.
The quake had a magnitude of nine, one of the biggest recorded in a century – and came a year after a dozen oarfish washed up on Japan’s coastline.
But scientists dispute such claims.
Uozu Aquarium keeper Kazusa Saiba told CNN last month that global warming or subtle changes in the ocean could be the cause.
The keeper said: “It could cause the current to stir and push creatures at the bottom to the surface.
“There is no scientific evidence at all for the theory that oarfish appear around big quakes.
“But we cannot 100 percent deny the possibility.”
This is not the first fishy incident to spark fears recently.
Thousands of headless fish with their bladders torn out were washed onto a German shore earlier this month.