UN and local agencies have issued conflicting tolls, and the final figure is likely to rise still higher.
One week after the storm, food and supplies are now beginning to reach survivors, but aid agencies say the logistics of distribution are enormous.
The Philippine government has defended its response to the disaster, one of the strongest storms ever on land.
The latest death toll of 3,621 issued by the National Disaster Risk Reduction and Management Council was up from the figure of 3,422 the interior secretary had given a few hours before.
The UN put the number of dead at 4,460. Officials said it was likely more bodies would be found as aid teams reached outlying areas.
Helicopters from a US aircraft carrier have been transporting supplies to the devastated town of Guiuan on the Pacific coast – the first to take the full force of the typhoon.
The carrier, USS George Washington, is expanding search-and-rescue operations and providing a platform for helicopters to move supplies.
Pallets loaded with food and water have been taken from the aircraft carrier to Tacloban, the capital of badly hit Leyte province, and Guiuan.
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