Stranded travellers were outraged and annoyed by the malfunction and lack of information given by airport staff.
A woman who was supposed to fly to Singapore said she spent several hours sitting in a plane on the tarmac.
She and her fellow passengers were eventually taken off the plane and offered hotel rooms.
"We were told it was a complete failure of radio comms at air traffic control," she told AFP.
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. Only in the PH. Sigh," Pangilinan wrote.
Manila passenger Daryll Delgado said she had managed to rebook her flight for a later date after a "frustrating" experience.
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.
More than 360 flights in and out of Manila were cancelled, diverted or delayed, affecting around 56,000 passengers.
