The power cuts began before dawn and affected heavily populated areas in Mindanao, home to a quarter of the country's nearly 100 million population.
"Reports indicate that the Mindanao grid experienced a disturbance at 3.53 am... (We are) still determining the cause and extent of the disturbance," the National Grid Corporation of the Philippines (NGCP) said in a statement.
Mindanao, the nation's main southern island which relies mostly on hydroelectricity, has been grappling with chronic power shortages for years.
The NGCP said at least 12 of Mindanao's key cities and provinces -- including major trading hubs -- were affected, although limited power was restored in some parts a few hours later.
Philippine Energy Secretary Jericho Petilla said repair crews were working to trace the cause of the interruption, stressing that he was confident power would return to all areas within the day.
"So far, there are no reports of damaged power plants," Petilla told DZBB radio in Manila. "They are ready to come back online to the grid, we just have to turn them (on) one by one."
"We are trying to figure out where" the source of the interruption was, he said, adding the outage was likely caused by a tripped transmission line.
An electricity shortage last year forced the NGCP to ration off supply in Mindanao, resulting in up to 12 hour daily blackouts which damaged the local economy as factories slowed production.
The power cuts on Thursday hit islanders just as they were getting ready for work.
"I had to keep using my lighter because the shops were still closed and we didn't have candles," said market vendor and mother-of-two Mary Villasenor from the southern Davao City.
"The kids had to go to school with wrinkled clothes because we couldn't plug in the flat iron," she said.