The blackout hit as many people began returning to the capital for work and school after the Christmas and New Year break.
Tens of thousands of travellers were stranded at Philippine airports after a power outage knocked out communication and radar equipment at the country's busiest hub in Manila, forcing hundreds of flights to be cancelled, delayed or diverted.
Aviation authorities detected a "technical issue" on Sunday morning involving the air traffic management centre at Manila's domestic and international airport.
More than 360 flights in and out of Manila were cancelled, diverted or delayed, affecting around 56,000 passengers.
There were chaotic scenes at check-in counters across the country as thousands of people tried to re-book tickets or find when their flights might take off.
Others who had boarded their aircraft before the glitch was announced waited for hours and were then disembarked.
Airport officials did not initially specify the cause of the problem.
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But transportation department secretary Jaime Bautista said the air traffic management centre, which controls inbound and outbound flights, "went down" due to a power outage that resulted in the loss of communication, radio, radar and internet.
"The secondary problem was the power surge due to the power outage which affected the equipment," he said.
Airport authorities said the air traffic management system was partially restored by 4:00 pm (0800 GMT) and flights were beginning to take off and land in Manila.
"The flight delays and diversions are only precautionary measures to ensure the safety of passengers, crew, and aircraft," the Civil Aviation Authority of the Philippines said.
Stranded travellers were outraged and annoyed by the malfunction and lack of information given by airport staff.
Tycoon Manny Pangilinan tweeted that he had been flying from Tokyo to Manila when the plane was diverted to Haneda due to "radar and navigation facilities" going down.
"6 hours of useless flying but inconvenience to travelers and losses to tourism and business are horrendous.
An AFP reporter in the southern city of Davao said travellers were advised not to go to the airport but many only found out their flights had been cancelled after they arrived to check in.