BBC
Entire neighbourhoods in Cagayan de Oro and Iligan cities were swept away.
The previous estimate for the missing was just 51 but officials say the new figure includes city migrant workers whose rural relatives did not immediately realise they were missing.
The authorities acknowledge that the new number may still not be accurate, reports the BBC's Kate McGeown in Manila.
Entire families who were killed may still not be accounted for and some of the missing may also be counted among the unidentified dead.
But, says our correspondent, it is clear that the scale of this disaster is far greater than the authorities originally thought.
The death toll from the disaster now stands at 1,080, the government says. Some 338,000 people have been affected and more than 10,000 homes damaged.
Tens of thousands of people are now living in evacuation centres.
Many of those who died were sleeping as Typhoon Washi caused rivers to burst their banks, leading to landslides.
Aid agencies have appealed for funds to help local people. The United Nations is seeking $28.6m (£18.2m) from donors to help provide water and sanitation to storm victims.
"We must improve this situation at the soonest possible time to avoid disease outbreaks that will further compound the hardships of the people already weakened by hunger, and grief from loss of family and friends," Soe Nyunt-U, acting UN humanitarian coordinator, told journalists in Manila on Thursday.
The government has been shipping coffins and aid to the storm-hit region in Mindanao
The Philippines government says 1,079 people are still missing in the wake of the devastating Typhoon Washi.
More than 1,000 others are known to have died in the storm, which struck Mindanao island on Saturday. Entire neighbourhoods in Cagayan de Oro and Iligan cities were swept away.
The previous estimate for the missing was just 51 but officials say the new figure includes city migrant workers whose rural relatives did not immediately realise they were missing.
The authorities acknowledge that the new number may still not be accurate, reports the BBC's Kate McGeown in Manila.
Entire families who were killed may still not be accounted for and some of the missing may also be counted among the unidentified dead.
But, says our correspondent, it is clear that the scale of this disaster is far greater than the authorities originally thought.
The death toll from the disaster now stands at 1,080, the government says. Some 338,000 people have been affected and more than 10,000 homes damaged.
Tens of thousands of people are now living in evacuation centres.
Many of those who died were sleeping as Typhoon Washi caused rivers to burst their banks, leading to landslides.
Aid agencies have appealed for funds to help local people. The United Nations is seeking $28.6m (£18.2m) from donors to help provide water and sanitation to storm victims.
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