The first quake of magnitude 7.4, in waters off the town of Manay in the province of Davao Oriental, triggered a tsunami alert for coasts within 300 km (186 miles) of the epicentre, but the warnings for the Philippines and Indonesia were subsequently lifted.
A second earthquake of magnitude 6.8 struck the same area seven hours later, triggering a new tsunami warning, with the country's seismology agency Phivolcs warning of possible waves that could be more than one metre (3.2 feet) higher than normal tides.
People living near coastal areas in the southern Philippines were "strongly advised to immediately evacuate" to higher ground, or move further inland, it said in an advisory.
Phivolcs Director Teresito Bacolcol described the twin earthquakes as a "doublet", two distinct earthquakes that occurred along a massive trench off the country's eastern seaboard.
There were initial reports of damage to homes, buildings and bridges, one official in Manay said, although the full extent of the damage in the Philippines was not immediately clear.
At least seven people were killed, civil defence official Ednar Dayanghirang said in a briefing. The fatalities were reported in towns and cities near the earthquake's epicentre.The twin quakes were among the strongest in recent years to hit the Philippines, which sits on the Pacific "Ring of Fire" and experiences more than 800 quakes each year.
It came two weeks after the Philippines experienced its deadliest earthquake in more than a decade with 74 people killed on the central island of Cebu following an offshore quake of magnitude 6.9.
A video posted on social media and verified by Reuters showed people in the city of Davao calmly holding on to parked vehicles that rocked from side to side as the ground shook, as metal gates rattled nearby.
A 7.4 magnitude earthquake struck off the southern coast of Philippines, prompting tsunami warnings from Philippine and Indonesian authorities.
Residents in coastal towns in central and southern Philippines were asked to evacuate as authorities warned of waves over a metre (3.3ft) above normal tide levels.
At least one person was killed in the earthquake on Friday morning, which also led to power cuts and classes being suspended in parts of the country.
The latest tremor comes just over a week after a 6.9 magnitude quake hit Philippine's central Cebu province, killing 74 people and injuring hundreds.Footage on local media show overhead network cables swaying as vehicles come to a standstill the moment the 7.5 magnitude quake struck.
Reporters observed a frenzy outside a hospital in Davao City, near the quake's epicentre, as patients were being treated outdoors in a carpark and crowds thronged the corridors.
A local governor described scenes of panic as tremors rattled his province.
"Some buildings were reported to have been damaged," Edwin Jubahib, governor of Davao Oriental province, told Philippine broadcaster DZMM. "It was very strong."
Richie Diuyen, who works at the local disaster agency in the town of Manay, said some students fainted after the quake and that it left her feeling dizzy.
"I am still scared and shook. We couldn't believe how strong the earthquake was. This was the first time I have experienced that," Ms Diuyen told the BBC.
The Philippines, which sits on the geologically unstable "Ring of Fire", has been reeling from a string of devastating natural disasters.
"Filipinos are now experiencing disaster fatigue from typhoons, volcanic minor eruptions and earthquakes," Dr Teresito Bacolcol, director of the Philippine volcanic agency Phivolcs, said in a media conference on Friday.
Dr Bacolcol called on Filipinos to "accept our reality" that "every now and then we will be jolted by earthquakes, volcanic eruptions and tsunamis".
"Instead of panicking, we have to prepare," he said.
Getty Images Rescuers helping a student onto a stretcher outside the Davao De Oro State College in DavaoGetty Images
The 7.4 magnitude earthquake led to power cuts and classes being suspended in parts of the Philippines
The earthquake in Cebu on 4 October was among the strongest and deadliest the nation has experienced in recent years, and has displaced some 80,000 people across the province.
Last month, a super typhoon pummelled through the country's north, killing 11 people.
Philippine authorities had warned of "destructive" and "life threatening" tsunami waves following Friday's earthquake, but the Pacific Tsunami Warning Center in Hawaii said about an hour later that the threat had passed.
Still, aftershocks with magnitudes ranging from 2.6 to 4.9 have continued rattling the southern region of Mindanao hours after the initial quake, Phivolcs reported.
In nearby Indonesia "minor tsunamis" were detected, with the highest reaching 17cm in the Talaud Islands in North Sulawesi.
Students on the Talaud Islands, an archipelago close to the Philippine border, have been sent home, but the situation remains calm, a local official told the BBC.
Indonesians urged people to "remain calm" and to stay away from buildings damaged by the earthquake.
With reporting by Arie Firdaus from Jakarta and Osmond Chia from Singapore
Map of where the 7.4 magnitude earthquake hit off the coast of southern Philippines on 10 October
'When I stand, I feel dizzy': Deadly earthquake leaves Filipinos struggling in ghost towns