The Japan Meteorological Agency had earlier warned the waves could reach a metre in height.
Orders to relocate were made in the Philippines, where there were no initial reports of significant wave damage or casualties despite continuing aftershocks.
The Philippine Institute of Volcanology and Seismology, Phivolcs, maintained that the risk of a tsunami remained.
"The warning has not been cancelled yet," it said in a statement to reporters.
People living near the coast of Surigao Del Sur and Davao Oriental provinces should "immediately evacuate" or "move farther inland," Phivolcs said in its initial warning.
"Boats already at sea during this period should stay offshore in deep waters until further advised," it said.
The two provinces are largely rural and not densely populated, unlike other parts of the Philippines.
Phivolcs said it was expecting some damage from the tremor, having initially said it did not expect any damage, and warned of aftershocks.
The area was quickly hit by more than two dozen aftershocks, the largest measuring magnitude 6.5, according to the European-Mediterranean Seismological Centre (EMSC).
Raymark Gentallan, police chief of the coastal town of Hinatuan, 30km from the earthquake's epicentre with a population of about 44,000, said power had been out since the quake struck.
"We're evacuating people away from coastal areas," he told Reuters, adding disaster response teams had not yet seen any casualties or damage.
James Soria, who owns a small hotel in Hinatuan, said there had been significant damage to his home.
"It's shaking again here now," he told Reuters, before the call was disconnected as another aftershock hit the area.
Photographs posted on social media by Hinatuan's local administration showed scores of residents and queues of vehicles moving towards higher ground, with one large shelter occupied by several dozen people.
Cosme Calejesan, 47, who lives in Surigao City, 185km from the epicentre, said there had been damage to his house but the structure was still intact.
"I was already asleep but I was woken up by the creaking sounds of my cabinets when the tremor occurred," he said.
"It was frightening. It was sudden and abrupt and I was worried for my children."
🔔— EMSC (@LastQuake) #Earthquake (#lindol) M7.5 occurred 30 km N of #Bislig (#Philippines) 29 min ago (local time 22:37:08). More info at:📱https://t.co/IbUfG7TFOL�https://t.co/RS7HTnB4Nt🖥https://t.co/r7lPuqvdsS pic.twitter.com/Djbko7l9RVDecember 2, 2023
Earthquakes are common in the Philippines, which lies on the "Ring of Fire", a belt of volcanoes circling the Pacific Ocean that is prone to seismic activity.
The US Geographic Survey said a quake of magnitude 7.6 struck at a depth of 32km at 10.37pm Philippines time on Saturday.
The Joint Australian Tsunami Warning Centre said there was no tsunami threat to the Australian mainland, islands or territories from the initial earthquake or aftershocks.
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