The typhoon has affected more than 213,000 people, demolished houses and stranded people in two Mindanao regions and parts of the Visayas region, according to the disaster agency. More than 179,000 people are in evacuation centers, it said.
A landslide in eastern Mindanao blocked a national highway, the news agency reported, leavening hundreds of people in buses, vans and cars stuck on the road.
Maintenance workers were using heavy equipment to clear the mud and rocks, said Dennis Flores, a spokesperson for the Department of Public Works and Highways cited by the news agency.
The tightly packed but fierce typhoon churned west northwest across the island, weakening slightly as it went, the Philippine Atmospheric, Geophysical and Astronomical Services Administration said.
By Wednesday morning, the center of the storm was approaching the outlying western island of Palawan. But it continued to soak a wide area with heavy rain, raising the risk of mudslides and flash floods elsewhere.
The storm, dubbed "Pablo" in the Philippines, had blown up into a super typhoon at one point Monday as it moved over the ocean, with sustained winds greater than 240 kph -- the equivalent of a Category 5 hurricane in the Atlantic Ocean, the Joint Typhoon Warning Center reported.
That wind speed is two and a half times the top winds of Severe Tropical Storm Washi, known in the Philippines as Sendong, whose heavy rains swept away entire villages in the same region in December 2011.
"Many emotional people in (Mindanao) trying to prepare for Pablo with Sendong fresh in their minds," Carin van der Hor, the Philippines director for the children's charity Plan International, wrote Monday on Twitter.
But local authorities have done a good job of relocating people out of vulnerable areas and preparing evacuation centers, said Gordon of the Red Cross.
Washi, on the other hand, caught many residents off guard. It was a weaker storm, but its torrential rain triggered landslides and flash floods in the middle of the night, when many people were sleeping. More than 1,200 people died and hundreds of thousands were left homeless, prompting a humanitarian crisis.
Ahead of Bopha's arrival on Tuesday, government agencies relocated more than 50,000 people to evacuation centers. They also moved millions of dollars worth of relief supplies into position for quick delivery to storm-hit regions and put emergency crews, the military and hospitals on standby.
School classes were suspended in many cities, and dozens of flights were canceled, according to the national disaster agency. Nearly 5,000 travelers were left stranded at ports across the country as of Wednesday because of disruption to ferry services.
Palau, a tiny island nation roughly 1,000 kilometers (600 miles) east of Mindanao, had a close shave with Bopha earlier in the week as the typhoon churned past, catching some outlying parts of the archipelago.
"It was headed right toward Palau," said Derek Williams, a meteorologist for the U.S. National Weather Service in Guam. But at the last minute, "it just turned to the west and fortunately went south of them," he said.
Bopha nonetheless brought down a lot of trees and caused widespread power outages in Palau, according to Williams.
"The fast movement of the system really prevented a lot of flooding," he said. "I think probably only a few inches of rain fell, so that's certainly good news, because Palau itself is susceptible to mudslides."
CNN's Sarita Harilela and Elizabeth Joseph, Michael Pearson and Neda Farshbaf contributed to this report.
Jovan Belcher had advanced from an undrafted free agent linebacker to NFL starter for the Kansas City Chiefs and played in every game since 2009. On Saturday, December 1, the 25-year-old star allegedly killed his girlfriend, then drove to the Chiefs' practice facility and took his own life. After the tragedy, teammat e Tony Moeaki tweeted, "One of everyone's favorite teammates including one of mine." Here's a look at his career with the Chiefs and tragic end: 
The Kansas City Chiefs kneel and pray before a game against the Carolina Panthers on Sunday, December 2, at Arrowhead Stadium in Kansas City, Missouri. 
Natalie Samson wears the No. 59 jersey, which was Jovan Belcher's number, as she stands for a moment of silence on Sunday. 
Players from the Kansas City Chiefs and Carolina Panthers gather at midfield Sunday for a prayer after the Chiefs' 27-21 win. 
A young fan holds a condolences sign for the Kansas City Chiefs prior to the team's game against the Carolina Panthers on Sunday. 
Before their game against the Carolina Pathers on Sunday, the Kansas City Chiefs pause for a moment of silence. 
After Belcher and his girlfriend's deaths, flags wave in the wind outside of The University of Kansas Hospital Training Complex used by the Kansas City Chiefs next to Arrowhead Stadium, on Saturday, December 1. 
No. 59 Belcher battles guard Clint Boling of the Cincinnati Bengals during the game at Arrowhead Stadium on November 18, 2012 in Kansas City. 
Belcher stretches before the game against the Oakland Raiders at Arrowhead Stadium on September 20, 2009, in Kansas City. 
The residence of Kasandra Perkins, Belcher's girlfriend, is seen on December 1, 2012, in Kansas City. 
Belcher during an NFL game against the Atlanta Falcons on September 9, 2012. 
Belcher brings down Buffalo Bills running back C.J. Spiller in the third quarter at Arrowhead Stadium on October 31, 2010. 
Belcher cools off from temperatures over 100 degrees during a training camp practice on the campus of Missouri Western State University in St. Joseph, Missouri, on August 1, 2011. 
The linebacker after a game against the Pittsburgh Steelers at Heinz Field on November 12, 2012 in Pittsburgh, Pennsylvania. The Steelers defeated the Chiefs 16-13. 
Belcher watches from the sidelines during his final game against the Denver Broncos at Arrowhead Stadium on November 25, 2012. 
Belcher in action during the game against the Cincinnati Bengals at on November 18, 2012, in Kansas City. 
