A grade-six pupil died after being plucked out from a collapsed chapel wall while a nine-year-old girl was killed when the concrete wall of a school collapsed, officials said.
A three-storey building caved in and some seaside cottages were destroyed by waves in La Libertad, Negros Oriental, near the epicenter of the quake 5 km (three miles) off the shore of Tayasan town and at a depth of 10 km, according to local calculations.
The U.S. Geological Survey had measured the quake at magnitude 6.7 and at a depth of 12.4 miles.
The volcanology and seismology institute lifted a tsunami alert. Some roads, bridges and houses sustained cracks, but major roads remained passable.
Television footage showed people scurrying out of buildings, residents converging in open spaces and frightened school children in tears.
"I have advised our people to return to their homes and stay calm. I appeal to our president for help. We're just recovering from Typhoon Sendong and now this earthquake," Negros Oriental Governor Roel Degamo said in a television interview, referring to a typhoon which killed about 1,250 people in the southern Philippines in December.
The quake was felt in areas within a radius of about 70 miles.
Over the weekend, the USGS also recorded a magnitude 5.6 quake off the shore of Samar province also in central Philippines and situated northwest of Negros.
The Philippines lies on the Pacific "Ring of Fire" and is prone to earthquakes and volcanic eruptions. A 7.8 magnitude quake in 1990 in the northern Philippines killed more than 1,600 people.