A few buildings collapsed and key infrastructure sustained quake damage in the city of General Santos on Monday, and tsunami damage was reported in at least one coastal village.
Smaller waves were measured in Indonesia and Palau and as far away as southern Japan.
"It's a major earthquake," Teresito Bacolcol, the director of the Philippine Institute of Volcanology and Seismology said, warning people to seek advise before returning to damaged buildings and houses that could collapse due to aftershocks.
"Our pick-up truck suddenly jerked and I thought we had a flat tyre," said Rod Sosmena, regional director of the Office of Civil Defence, told The Associated Press from the hard-hit port city of General Santos, where he was travelling when the quake struck at 7.37am.
"The shaking was very strong and people dashed out of houses into the streets," Sosmena said.
General Santos is a port city of more than 700,000 people that is a regional hub for the tuna export industry and other commerce.
The strongest quake to strike the Philippines this year was centred at sea off Mindanao island at a depth of 33km.
Philippine President Ferdinand Marcos Jr ordered the cancellation of classes and directed disaster-response agencies to immediately get to work in quake-hit provinces, saying "the national government is moving and we will not leave Mindanao behind".
The Pacific Tsunami Warning Center said the threat of a tsunami largely passed about five hours after the quake.
Philippine officials also lifted a tsunami warning by mid-afternoon.
Six shanties on stilts were damaged in a coastal village in Zamboanga del Sur due to the quake and taller waves, officials said.
At least 19 people were killed, mostly in collapsed buildings and landslides, while thousands of villagers were displaced, Office of Civil Defence spokesman Junie Castillo said.
Among the dead were seven people in General Santos, where a few small buildings collapsed or were severely damaged, Sosmena said.
The other deaths were caused by falling debris, a damaged mosque and a landslide in the southern provinces of Sarangani, South Cotabato and Davao Occidental and on Balut Island.
Sosmena said authorities were checking reports of some students being trapped in a two-storey school that collapsed in General Santos.
Public schools had reopened nationwide Monday after the summer holidays.
Dayanghirang said more than 100 students attending morning flag-raising ceremonies in his southern region sustained bruises and some fainted in panic.
The international airport in General Santos was temporarily shut, and 17 domestic flights were cancelled, the Civil Aviation Authority of the Philippines said.
Waves of 1m were generally monitored in the provinces of Sultan Kudarat and Sarangani.
A 1.4m wave was monitored at one time in the coastal area of Kiamba town in Sarangani, Bacolcol said.
The quake was also felt in Malaysia's Sabah state on Borneo island. Sabah is just a boat ride away from southern Philippines.
An 83cm tsunami was measured by a gauge off Indonesia's Sulawesi island, and the PTWC said 30cm waves were measured in Palau.
Waves up to 20cm were detected on the remote Japanese island of Chichijima and the central Japanese town of Kushimoto, the Japan Meteorological Agency said.
The US Geological Survey reported the depth of the original quake at 55km.
Aftershocks as strong as 6.5 magnitude were recorded.
The Philippines, one of the world's most disaster-prone countries, is often hit by earthquakes and volcanic eruptions due to its location on the Pacific "Ring of Fire," an arc of seismic faults around the ocean.
