The weather agency said last week a huge earthquake was more likely in the aftermath of a magnitude 7.1 jolt in the south on Thursday, which left at least 15 people injured.
The advisory, the first of its kind, doesn't mean a colossal tremor is imminent, but that the risk of such an event has now been elevated, if still low, authorities have said.
Subject to the warning is the so-called "Nankai Trough" 800-kilometre (500-mile) undersea zone that runs from Shizuoka, west of Tokyo, to the southern tip of Kyushu island.
In western Kochi, among the regions projected to be hit hardest, at least 9,400 people have cancelled their hotel bookings since the alert was issued last week, according to a local hotel union.
The cancellations covering the period August 9 to 18, amount to a loss of around 140 million yen ($948,000) in revenue, Susumu Nishitani, a union representative told AFP.
The warning coincided with Japan's annual "obon" holiday, a busy season for tourism businesses when many Japanese visit their hometowns and pay respects to ancestors.
"Normally all hotels and inns in our city would be fully booked at this time of the year", Nishitani said.
Thousands more cancellations are expected in the neighbouring Matsuyama city's Dogo Onsen, one of the hot springs believed to have inspired animation studio Ghibli's globally-acclaimed film "Spirited Away", public broadcaster NHK said.
The megaquake advisory is set to be lifted on Thursday this week if no abnormalities in seismic activity are detected, local media have reported.
"It is our slight hope that new reservations will start trickling in once the warning is lifted," Nishitani said.
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