Several buildings including a state college were heavily damaged and a bridge also collapsed.
Terrified residents fled to higher ground after the quake, fearing that a tsunami would hit the coastal city of over 152,000 people while others spent the night in parking lots and open fields.
The casualties occurred in Surigao del Norte province on the northern tip of Mindanao island which was closest to the epicentre of the quake, which struck at 10.03pm.
At least 30 aftershocks have rattled the surrounding areas in the hours following the quake, the Institute measured.
Surigao's airport was also shut down after officials noticed cracks on the runway.
Provincial disaster monitoring chief Ramon Gotinga said residents were still on edge. "At the slightest shaking, they run out in the streets", he said.
White House Says Justin Trudeau Will Visit President Trump Monday
Trump adviser Kellyanne Conway also told CNN on Tuesday that Trudeau would come to the White House "next week". The White House meeting was long expected, despite signs of tension between Trump and Trudeau.
At least six people were killed, mostly after being struck by falling debris and concrete walls, provincial disaster-response official Gilbert Gonzales said.
The Philippines sits on the highly seismically active zone "Pacific Ring of Fire" where many continental plates on the earth's crust keep colliding.
Almost 100 aftershocks were reported, according to official figures. The quake was centered about 14 kilometers (8 miles) northwest of the provincial capital of Surigao at a relatively shallow depth of 11 kilometers (6.8 miles).
The quake, which hit the southern region of Philippines damaged buildings and an airport and knocked out power in vast areas, officials on Saturday said, according to Associated Press reports.
Matugas confirmed only helicopters can land at Surigao airport.
The tremor was felt also felt at Intensity 2 in Bislig, Surigao Del Sur and at Intensity 1 in the cities of Cebu and Cagayan de Oro City.